Genetic dissection of heterochromatin in Drosophila: the role of basal X heterochromatin in meiotic sex chromosome behaviour

Meiotic, genomic and evolutionary properties of crossover distribution in Drosophila yakuba

The number and location of crossovers across genomes are highly regulated during meiosis, yet the key components controlling them are fast evolving, hindering our understanding of the mechanistic causes and evolutionary consequences of changes in crossover rates. Drosophila melanogaster has been a model species to study meiosis for more than a century, with an available high-resolution crossover map that is, nonetheless, missing for closely related species, thus preventing evolutionary context. Here, we applied a novel and highly efficient approach to generate whole-genome high-resolution crossover maps in D. yakuba to tackle multiple questions that benefit from being addressed collectively within an appropriate phylogenetic framework, in our case the D. melanogaster species subgroup. The genotyping of more than 1,600 individual meiotic events allowed us to identify several key distinct properties relative to D. melanogaster. We show that D. yakuba, in addition to higher crossover rates than D. melanogaster, has a stronger centromere effect and crossover assurance than any Drosophila species analyzed to date. We also report the presence of an active crossover-associated meiotic drive mechanism for the X chromosome that results in the preferential inclusion in oocytes of chromatids with crossovers. Our evolutionary and genomic analyses suggest that the genome-wide landscape of crossover rates in D. yakuba has been fairly stable and captures a significant signal of the ancestral crossover landscape for the whole D. melanogaster subgroup, even informative for the D. melanogaster lineage. Contemporary crossover rates in D. melanogaster, on the other hand, do not recapitulate ancestral crossovers landscapes. As a result, the temporal stability of crossover landscapes observed in D. yakuba makes this species an ideal system for applying population genetic models of selection and linkage, given that these models assume temporal constancy in linkage effects. Our studies emphasize the importance of generating multiple high-resolution crossover rate maps within a coherent phylogenetic context to broaden our understanding of crossover control during meiosis and to improve studies on the evolutionary consequences of variable crossover rates across genomes and time.

Female Meiosis: Synapsis, Recombination, and Segregation in Drosophila melanogaster

A century of genetic studies of the meiotic process in Drosophila melanogaster females has been greatly augmented by both modern molecular biology and major advances in cytology. These approaches, and the findings they have allowed, are the subject of this review. Specifically, these efforts have revealed that meiotic pairing in Drosophila females is not an extension of somatic pairing, but rather occurs by a poorly understood process during premeiotic mitoses. This process of meiotic pairing requires the function of several components of the synaptonemal complex (SC). When fully assembled, the SC also plays a critical role in maintaining homolog synapsis and in facilitating the maturation of double-strand breaks (DSBs) into mature crossover (CO) events. Considerable progress has been made in elucidating not only the structure, function, and assembly of the SC, but also the proteins that facilitate the formation and repair of DSBs into both COs and noncrossovers (NCOs). The events that control the decision to mature a DSB as either a CO or an NCO, as well as determining which of the two CO pathways (class I or class II) might be employed, are also being characterized by genetic and genomic approaches. These advances allow a reconsideration of meiotic phenomena such as interference and the centromere effect, which were previously described only by genetic studies. In delineating the mechanisms by which the oocyte controls the number and position of COs, it becomes possible to understand the role of CO position in ensuring the proper orientation of homologs on the first meiotic spindle. Studies of bivalent orientation have occurred in the context of numerous investigations into the assembly, structure, and function of the first meiotic spindle. Additionally, studies have examined the mechanisms ensuring the segregation of chromosomes that have failed to undergo crossing over.

Whole-Genome Analysis of Individual Meiotic Events in Drosophila melanogaster Reveals That Noncrossover Gene Conversions Are Insensitive to Interference and the Centromere Effect

A century of genetic analysis has revealed that multiple mechanisms control the distribution of meiotic crossover events. In Drosophila melanogaster, two significant positional controls are interference and the strongly polar centromere effect. Here, we assess the factors controlling the distribution of crossovers (COs) and noncrossover gene conversions (NCOs) along all five major chromosome arms in 196 single meiotic divisions to generate a more detailed understanding of these controls on a genome-wide scale. Analyzing the outcomes of single meiotic events allows us to distinguish among different classes of meiotic recombination. In so doing, we identified 291 NCOs spread uniformly among the five major chromosome arms and 541 COs (including 52 double crossovers and one triple crossover). We find that unlike COs, NCOs are insensitive to the centromere effect and do not demonstrate interference. Although the positions of COs appear to be determined predominately by the long-range influences of interference and the centromere effect, each chromosome may display a different pattern of sensitivity to interference, suggesting that interference may not be a uniform global property. In addition, unbiased sequencing of a large number of individuals allows us to describe the formation of de novo copy number variants, the majority of which appear to be mediated by unequal crossing over between transposable elements. This work has multiple implications for our understanding of how meiotic recombination is regulated to ensure proper chromosome segregation and maintain genome stability.

The effect of an unusual chromosome architecture on disjunction and non-disjunction in Drosophila

Two homologous autosomes of Drosophila that were attached to form a single entire compound autosome II were found to affect the segregation of the sex chromosomes in both males and females. The compound segregated nearly always from an attachedX.Ychromosome in males with no other sex chromosome. When two sex chromosomes were present together with the compound they differed in their tendency to segregate from the compound. In males theX.Ychromosome segregated more often from the compound than did theYchromosome, and theYchromosome segregated more often from the compound than did the regularXchromosome. In females theX.Ysegregated more often from the compound than did the regularXchromosome. This preferential segregation in females was observed for exchangeXchromosomes as well as for the non-exchange chromosomes.

In the presence of the compound the frequency of primary non-disjunction of the sex chromosomes was elevated in both females and males; usually both sex chromosomes segregatedfromthe compound and only rarelywithit.

Flies devoid of most of the proximal heterochromatin of the sex chromosomes die. However, when the compound autosome was present some such flies survived. This indicates that a segment of the proximal heterochromatin of the sex chromosomes was intercalated into the compound when it was constructed. It was concluded that the segment intercalated into the compound carries specific sites for sex chromosome disjunction. Specific sites determine sex chromosome disjunction in males. In females they determine the disjunction of the sex chromosomes in cooperation with exchange pairing.

Heterochromatin-mediated association of achiasmate homologs declines with age when cohesion is compromised

Normally, meiotic crossovers in conjunction with sister-chromatid cohesion establish a physical connection between homologs that is required for their accurate segregation during the first meiotic division. However, in some organisms an alternative mechanism ensures the proper segregation of bivalents that fail to recombine. In Drosophila oocytes, accurate segregation of achiasmate homologs depends on pairing that is mediated by their centromere-proximal heterochromatin. Our previous work uncovered an unexpected link between sister-chromatid cohesion and the fidelity of achiasmate segregation when Drosophila oocytes are experimentally aged. Here we show that a weak mutation in the meiotic cohesion protein ORD coupled with a reduction in centromere-proximal heterochromatin causes achiasmate chromosomes to missegregate with increased frequency when oocytes undergo aging. If ORD activity is more severely disrupted, achiasmate chromosomes with the normal amount of pericentric heterochromatin exhibit increased nondisjunction when oocytes age. Significantly, even in the absence of aging, a weak ord allele reduces heterochromatin-mediated pairing of achiasmate chromosomes. Our data suggest that sister-chromatid cohesion proteins not only maintain the association of chiasmate homologs but also play a role in promoting the physical association of achiasmate homologs in Drosophila oocytes. In addition, our data support the model that deterioration of meiotic cohesion during the aging process compromises the segregation of achiasmate as well as chiasmate bivalents.

Isolation and cytogenetic characterization of male meiotic mutants of Drosophila melanogaster

Proper segregation of homologous chromosomes in meiosis I is ensured by pairing of homologs and maintenance of sister chromatid cohesion. In male Drosophila melanogaster, meiosis is achiasmatic and homologs pair at limited chromosome regions called pairing sites. We screened for male meiotic mutants to identify genes required for normal pairing and disjunction of homologs. Nondisjunction of the sex and the fourth chromosomes in male meiosis was scored as a mutant phenotype. We screened 2306 mutagenized and 226 natural population-derived second and third chromosomes and obtained seven mutants representing different loci on the second chromosome and one on the third. Five mutants showed relatively mild effects (<10% nondisjunction). mei(2)yh149 and mei(2)yoh7134 affected both the sex and the fourth chromosomes, mei(2)yh217 produced possible sex chromosome-specific nondisjunction, and mei(2)yh15 and mei(2)yh137 produced fourth chromosome-specific nondisjunction. mei(2)yh137 was allelic to the teflon gene required for autosomal pairing. Three mutants exhibited severe defects, producing >10% nondisjunction of the sex and/or the fourth chromosomes. mei(2)ys91 (a new allele of the orientation disruptor gene) and mei(3)M20 induced precocious separation of sister chromatids as early as prometa-phase I. mei(2)yh92 predominantly induced nondisjunction at meiosis I that appeared to be the consequence of failure of the separation of paired homologous chromosomes.

Isolation and Cytogenetic Characterization of Male Meiotic Mutants of Drosophila melanogaster

Proper segregation of homologous chromosomes in meiosis I is ensured by pairing of homologs and maintenance of sister chromatid cohesion. In male Drosophila melanogaster, meiosis is achiasmatic and homologs pair at limited chromosome regions called pairing sites. We screened for male meiotic mutants to identify genes required for normal pairing and disjunction of homologs. Nondisjunction of the sex and the fourth chromosomes in male meiosis was scored as a mutant phenotype. We screened 2306 mutagenized and 226 natural population-derived second and third chromosomes and obtained seven mutants representing different loci on the second chromosome and one on the third. Five mutants showed relatively mild effects (&lt;10% nondisjunction). mei(2)yh149 and mei(2)yoh7134 affected both the sex and the fourth chromosomes, mei(2)yh217 produced possible sex chromosome-specific nondisjunction, and mei(2)yh15 and mei(2)yh137 produced fourth chromosome-specific nondisjunction. mei(2)yh137 was allelic to the teflon gene required for autosomal pairing. Three mutants exhibited severe defects, producing &gt;10% nondisjunction of the sex and/or the fourth chromosomes. mei(2)ys91 (a new allele of the orientation disruptor gene) and mei(3)M20 induced precocious separation of sister chromatids as early as prometaphase I. mei(2)yh92 predominantly induced nondisjunction at meiosis I that appeared to be the consequence of failure of the separation of paired homologous chromosomes.

The license to pair: identification of meiotic pairing sites in Drosophila

Sites for pairing and segregation of achiasmatic bivalents have been characterized in both male and female meiosis in Drosophila melanogaster. The major sex chromosome pairing site in male meiosis corresponds to the intergenic spacer repeats of the rDNA arrays, which are located in the heterochromatin of the X and Y. The sex chromosome pairing sites in females are also heterochromatic, but involve different repeated sequences. In males, weak pairing sites are widely distributed along euchromatin but not heterochromatin of chromosome 2, an autosome. One strong site for male meiotic pairing has been identified on chromosome 2; it overlaps with the his locus, which contains the repetitive structural genes for the histones. In females the sites for pairing of chromosome 4, another autosome, are restricted to the heterochromatin. Thus for both sex chromosomes and autosomes, sites for achiasmatic pairing are heterochromatic in females but euchromatic (except for the rDNA) in males. The possible roles of sequence repetition and of transcription in chromosome pairing are discussed.

The centric region of the X chromosome rDNA functions in male meiotic pairing in Drosophila melanogaster

In Drosophila melanogaster males, sex chromosome pairing at meiosis is ensured by so-called pairing site(s) located discretely in the centric heterochromatin. The property of the pairing sites is not well understood. Recently, an hypothesis has been proposed that 240 bp repeats in the nontranscribed spacer region of rDNA function as the pairing sites in male meiosis. However, considerable cytogenetic evidence exists that is contrary to this hypothesis. Hence, the question is whether the chromosomal rDNA clusters, in which a high copy number of 240 bp repeats exists, are involved in the pairing. In order to resolve the problem we X-rayed Drosophila carrying the X chromosome inversion In(1)scV2L sc8R and generated free, mini-X chromosomes carrying a substantial amount of rDNA. We defined cytogenetically the size of the mini-chromosomes and studied their meiotic behavior. Our results demonstrate that the heterochromatin at the distal end of the inversion, whose length is approximately 0.4 times that of the fourth chromosome, includes a meiotic pairing site in the male. We discuss the cytological location of the pairing site and the possible role of rDNA in meiotic pairing.

Meiosis in Drosophila males. I. The question of separate conjunctive mechanisms for the XY and autosomal bivalents

The conjunctive mechanism of the XY bivalent is believed to differ from that of the autosomal bivalents in the achiasmate Drosophila melanogaster male. It has been proposed that hypothetical cohesive elements, termed collochores, hold the X and Y chromosomes together at or near their nucleolar organizing regions (NORs) and that collochores are not exhibited by autosomal bivalents. In electron micrographs, unique fibrillar material is observed between the X and Y chromosomes at the synaptic site. Recently, the 240 bp nontranscribed spacer associated with rRNA genes at the NOR has been implicated as the essential DNA sequence for XY pairing. To test whether this DNA sequence is always associated with XY pairing and to determine its relationship to the unique fibrillar material, we studied the XY bivalent in Drosophila simulans. The D. simulans Y chromosome has few, if any, rRNA genes, but does have a large block (3,000 kb or 12,500 copies) of the nontranscribed spacer repeat located at the distal end of its long arm. This is in contrast to the D. melanogaster Y, which has the repeat located among rRNA genes on its short arm. Using light and electron microscopy, we show that the X does indeed pair with the distal end of the long arm of the D. simulans Y. However, no fibrillar material is evident in serial thin sections of the D. simulans XY bivalent, suggesting that this material (in D. melanogaster) may be remnants of the NOR rather than a morphological manifestation of the hypothetical collochores.(ABSTRACT TRUNCATED AT 250 WORDS)

Meiotic mutations from natural populations of Drosophila melanogaster

Two meiotic genes from natural populations are described. A female meiotic mutation, mei(1)g13, mapped to 17.4 on the X chromosome, causes nondisjunction of all homologs except for the fourth chromosomes. In addition, it reduces recombination by 10% in the homozygotes and causes 18% increased recombination in the heterozygotes. A male meiotic mutation, mei-1223m144, is located on the third chromosome. Although this mutation causes nondisjunction of all chromosomes, each chromosome pair exhibits a different nondisjunction frequency. Large variations in the sizes of the premature sperm heads observed in the homozygotes may reflect irregular meiotic pairing and the subsequent abnormal segregation, resulting in aneuploid chromosome complements.

Cytogenetical localization of Zygotic hybrid rescue (Zhr), a Drosophila melanogaster gene that rescues interspecific hybrids from embryonic lethality

Hybrid females from crosses between Drsophila melanogaster males and females of its sibling species, D. simulans, D. mauritiana, or D. sechellia die as embryos. This lethality is believed to be caused by incompatibility between the X chromosome of D. melanogaster and the maternal cytoplasm. Zygotic hybrid rescue (Zhr) prevents this embryonic lethality and has been cytogenetically mapped to a proximal region of the X chromosome of D. melanogaster, probably in the centromeric heterochromatin. We have carried out high resolution cytological mapping of Zhr using deficiencies and duplications of the X heterochromatin. Deletions of the Zhr+ gene from the hybrid genome exhibit the Zhr phenotype. On the contrary, addition of the wild-type gene to the hybrid genome causes embryonic lethality, regardless of sex. The Zhr locus has been narrowed down to the region covered by Dp(1;f)1162 but not covered Dp(1;f)1205, a chromosome carrying a duplication of heterochromatin located slightly distal to the In(1)sc8 heterochromatic break-point.

Synthesis of free X duplications carrying a specific region of the centromeric heterochromatin in Drosophila melanogaster

Free X duplication chromosomes of Drosophila melanogaster were synthesized by X-ray irradiating the In(1)scL8Lsc8R chromosome which has a deletion in the distal half of hA and the proximal half of hB of the centromeric heterochromatin. Fifty-nine duplications have been isolated and cytogenetically analyzed. They all carry wild-type allele of the yellow gene, y+, which should come from the distal tip of In(1)scL8Lsc8R. They appear to be telocentric and predominantly heterochromatic. Majority of the duplications, especially in the classes MEDIUM and LARGE, can pair with XYL.YS in the male meiosis, indicating that they carry male meiotic pairing site(s) that is known to be located exclusively in the X heterochromatin. Complementation test in the males, Df(1)svr, v/Dp, y+, demonstrates that most of the duplications in the classes MEDIUM and LARGE carry euchromatin enough to cover the deletion. The portion of the euchromatin should be of the very proximal region close to the irradiated X chromosome centromere.

There are two mechanisms of achiasmate segregation in Drosophila females, one of which requires heterochromatic homology

There are numerous examples of the regular segregation of achiasmate chromosomes at meiosis I in Drosophila melanogaster females. Classically, the choice of achiasmate segregational partners has been thought to be independent of homology, but rather made on the basis of availability or similarities in size and shape. To the contrary, we show here that heterochromatic homology plays a primary role in ensuring the proper segregation of achiasmate homologs. We observe that the heterochromatin of chromosome 4 functions as, or contains, a meiotic pairing site. We show that free duplications carrying the 4th chromosome pericentric heterochromatin induce high frequencies of 4th chromosome nondisjunction regardless of their size. Moreover, a duplication from which some of the 4th chromosome heterochromatin has been removed is unable to induce 4th chromosome nondisjunction. Similarly, in the absence of either euchromatic homology or a size similarity, duplications bearing the X chromosome heterochromatin also disrupt the segregation of two achiasmate X chromosome centromeres. Although heterochromatic regions are sufficient to conjoin nonexchange homologues, we confirm that the segregation of heterologous chromosomes is determined by size, shape, and availability. The meiotic mutation Axs differentiates between these two processes of achiasmate centromere coorientation by disrupting only the homology-dependent mechanism. Thus there are two different mechanisms by which achiasmate segregational partners are chosen. We propose that the absence of diplotene-diakinesis during female meiosis allows heterochromatic pairings to persist until prometaphase and thus to co-orient homologous centromeres. We also propose that heterologous disjunctions result from a separate and homology-independent process that likely occurs during prometaphase. The latter process, which may not require the physical association of segregational partners, is similar to those observed in many insects, in Saccharomyces cerevisiae and in C. elegans males. We also suggest that the physical basis of this process may reflect known properties of the Drosophila meiotic spindle.

Meiotic pairing constraints and the activity of sex chromosomes

The state of activity and condensation of the sex chromosomes in gametocytes is frequently different from that found in somatic cells. For example, whereas the X chromosomes of XY males are euchromatic and active in somatic cells, they are usually condensed and inactive at the onset of meiosis; in the somatic cells of female mammals, one X chromosome is heterochromatic and inactive, but both X chromosomes are euchromatic and active early in meiosis. In species in which the female is the heterogametic sex (ZZ males and ZW females), the W chromosome, which is often seen as a condensed chromatin body in somatic cells, becomes euchromatic in early oocytes. We describe an hypothesis which can explain these changes in the activity and condensation of sex chromosomes in gametocytes. It is based on the fact that normal chromosome pairing seems to be essential for the survival of sex cells; chromosomal anomalies resulting in incomplete pairing during meiosis usually result in gametogenic loss. We argue that the changes seen in the sex chromosomes reflect the need to avoid pairing failure during meiosis. Pairing normally requires structural and conformational homology of the two chromosomes, but when the regions is avoided when these regions become heterochromatinized. This hypothesis provides an explanation for the changes found in gametocytes both in species with male heterogamety and those with female heterogamety. It also suggests possible reasons for the frequent origin of large supernumerary chromosomes from sex chromosomes, and for the reported lack of dosage compensation in species with female heterogamety.

DNA sequence adjacent to and specific for the 1.672 g/cm3 satellite DNA in the Drosophila genome

The Drosophila genome contains nearly 2.8 X 10(4) kilobases of satellite DNA. This simple sequence satellite DNA is contained within transcriptionally inactive heterochromatin that is distributed among all chromosomes with a concentration at the centromeres and along the length of the Y chromosome. To investigate the relationship of the satellite DNA with the surrounding sequences, we have isolated a satellite junction sequence that is repetitive and specifically adjacent to the 1.672 g/cm3 satellite DNA. It is conserved between strains of Drosophila melanogaster and localized to the chromocenter of polytene chromosomes. The characteristics of this sequence suggest a functional role involving the specific organization of large regions of chromosomes.

Segregation of centric Y-autosome translocations in Drosophila melanogaster. I. Segregation determinants in males

A special screening procedure for the detection of induced Y-autosome translocations with centric breakpoints was applied. A series of Experimental stocks was constructed, each containing a different half of one of the induced T(Y; 2)'s (T element). The three other elements that were involved in the segregation experiments in each stock were a sex chromosome (X element), an inverted chromosome 2 (A element), and a free arm of chromosome 2 (F element). It is not feasible to determine the relative frequencies of all the 16 possible gamete types by mating an Experimental stock to one tester, nor to different testers that have each at least one class of progeny of the same genotype. Each Experimental stock was mated to four different Tester stocks and the data were calibrated so that a coherent segregation pattern could be obtained.

Segregation patterns in meiosis of males from 15 Experimental stocks, each with a different T element were studied. In most Experimental stocks the T element was of the left autosomal arm, while the F element was of the right autosomal arm. In four Experimental stocks the X element segregated independently of the A, F and T elements. In these Group 1 stocks, both the F and the T elements disjoined regularly from the A element. It was concluded that the T element of these stocks had no sex-chromosome disjunction determinants (‘S-determinants’) to interact with the determinants on the X element. Both the T elements and the F elements carried autosomal disjunction determinants (‘H-determinants’) that secured the segregation of the autosomal elements. The H-determinants of the left autosomal arm were qualitatively different from those of the right arm.

In the remaining 11 Group-2 Experimental stocks the X and T elements disjoined regularly, indicating the presence of S-determinants on the T elements of these stocks. The segregation of the T and the A elements in these stocks varied from nearly complete dependence to complete independence. It was concluded that this gradation reflected differences in the quantity of H-determinants present on the T elements of these Experimental stocks. It was impossible to discriminate between a model of continuous H determinants activity and one of a finite discrete number of determinants. The results do not agree with the claim that there are no autosomal disjunction determinants in the proximal heterochromatin of chromosome 2.

The S-determinants on theBsYy+chromosome were located both adjacent to the centromere and distally on the long arm. The latter were probably translocated to the Y chromosome together with theBsmarker.

The mechanism of meiotic homologue pairing

Homologous chromosome pairing involves the moving together of matching chromosomes or chromosome segments across substantial distances within a nucleus. Although the time in the life cycle of initial association of homologues varies among organisms, it may well be that similar underlying mechanisms for its occurrence prevail throughout sexually reproducing eukaryotes. The means by which pairing its accomplished is in no case understood. In the apparent absence of a long range specific force of attraction, simple partial models have been proposed which relay for the most part upon interactions of chromosome ends (telomeres) with specialized portions of the nuclear envelope. While such interactions, as well as the persistence of chromosome orientation established by mitotic anaphase poleward movement of centromere regions, may provide in many cases for closer than random positioning of some parts of homologues, the distances remaining to be traversed are still long range in physical-chemical terms. Also, the specific pairing observed in some kinds of rearranged segments is not facilitated by such circumstances, even if synapsis is initiated at available homologous telomere pairs and proceeds to completion by a "zip-up" process. A unified, more complex model is considered which is designed to accommodate the various relevant findings. It invokes the interaction of intranuclear structures with intercalary and/or terminal chromosomal pairing sites, e.g. filamentous structures which specifically bind to these, and a contractile system involving proteins such as actin and myosin to draw homologues together.

Meiosis in Drosophila melanogaster. IV. The conjunctive mechanism of the XY bivalent

Chromosome pairing during meiosis I in D. melanogaster males was investigated ultrastructurally by examining complete bivalents in electron micrographs of serial thin sections. The XY bivalent is characterized by the presence of the unique material located between the two half-bivalents at the site of synapsis. The material has a fibrillar appearance and is less electron dense than the surrounding chromatin. XY bivalents in XYY males and XY bivalents containing the X chromosome, In (1) sc4LSC8R, where the pairing sites of the X chromosome are inverted and partially deleted also possess this material. The material is not associated with autosomal bivalents and may represent a morphological manifestation of the hypothetical cohesive elements (collochores) which are thought to function in conjunction of the X and Y chromosomes (Cooper, 1964).

The cytogenetic boundaries of the rDNA region within heterochromatin in the X chromosome of Drosophila melanogaster and their relation to male meiotic pairing sites

The proximal breakpoints of the inversion chromosomesIn(1)ωm4andIn(1)m51bwere shown, byin situhybridization, to define the boundaries of the ribosomal DNA region located within theXchromosome heterochromatin (Xh). We estimate thatat least95% of the rDNA is located between theIn(1)ωm4andIn(1)ωm51bproximal breakpoints. In contrast only 60–70% of the Type I intervening sequences located inXhare located between these breakpoints. The Type I intervening sequences in the rDNA region occur as inserts in the 28S rRNA sequences while the remainder of the sequences are distal to theIn(1)ωm4breakpoint and not associated with rRNA genes.

The regions of Xh which contain rDNA and Type I intervening sequences were related to regions shown by Cooper (1964) to contribute to meiotic pairing between theXandYchromosomes in male Drosophila. We demonstrate that the rRNA coding region contributes toX/Ypairing. However, no single region of Xh is required for fidelity of male meiotic pairing of the sex chromosomes.

Nucleotide sequences of highly repeated DNAs; compilation and comments

The nucleotide sequence data from highly repeated DNAs of inverte-brates and mammals are summarized and briefly discussed. Very similar conclusions can be drawn from the two data bases. Sequence complexities can vary from 2 bp to at least 359 bp in invertebrates and from 3 bp to at least 2350 bp in mammals. The larger sequences may or may not exhibit a substructure. Significant sequence variation occurs for any given repeated array within a species, but the sources of this heterogeneity have not been systematically partitioned. The types of alterations in a basic repeating unit can involve base changes as well as deletions or additions which can vary from 1 bp to at least 98 bp in length. These changes indicate that sequenceper seis unlikely to be under significant biological constraints and may sensibly be examined by analogy to Kimura's neutral theory for allelic variation. It is not possible with the present evidence to discriminate between the roles ofneutralandselectivemechanisms in the evolution of highly repeated DNA.

Tandemly repeated arrays are constantly subjected to cycles of amplification and deletion by mechanisms for which the available data stem largely from ribosomal genes. It is a matter of conjecture whether the solutions to the mechanistic puzzles involved in amplification or rapid redeployment of satellite sequences throughout a genome will necessarily give any insight into biological functions.

The lack of significant somatic effects when the satellite DNA content of a genome is significantly perturbed indicates that the hunt for specific functions at thecellularlevel is unlikely to prove profitable.

The presence or in some cases theamountof satellite DNA on a chromosome, however, can have significant effects in the germ line. There the data show that localized condensed chromatin, rich in satellite DNA, can have the effect of rendering adjacent euchromatic regionsrec−, or of altering levels of recombination on different chromosomes. No data stemming from natural populations however are yet available to tell us if these effects are of adaptive or evolutionary significance.

Restriction endonuclease and molecular analyses of three rat genomes with special reference to chromosome rearrangement and speciation problems

When differences are found between related species of organisms, it is often assumed that the differences themselves are causal factors either in speciation itself or in processes related to speciation. Two recent proposals on the functions of satellite DNA (Hatch et al., 1976 and Fry and Salser 1977) are that (a) large amounts of satellite DNA are important in facilitating chromosome rearrangements and hence cytogenetic evolution, and (b) satellite DNA differences between homologous chromosomes lead to pairing difficulties and are important in generating infertility barriers and hence speciation. If these proposals were to have some generality, one could expect organisms with very low amounts of highly repeated DNA to exhibit few chromosome rearrangements and to be evolutionarily conservative in a cytogenetic sense.--We have chosen two very closely related species of rat which are phenotypically almost indistinguishable and which have undergone massive genome reorganization. They differ by 11 major centric rearrangements (2n = 32, 2n = 50). We have characterised their genomes by restriction endonuclease digestions, thermal denaturations, analytical ultracentrifugations and reassociation techniques, and have found that they have virtually no highly repeated DNA. Thus the 11 major chromosomal rearrangements have been fixed in present day genomes with hardly any highly repeated DNA, centric or otherwise.--It appears therefore, that a large amount of highly repeated DNA is not obligatory for the formation and fixation of chromosome rearrangements. In addition, the existing literature reveals that one can find almost any situation at all, from species groups with high amounts of satellite DNA and no gross chromosomal rearrangements, to ones such as those described here, with tiny amounts of highly repeated DNA and massive chromosomal reorganisation. Since direct experimental data indicates that satellite DNA differences per se between homologous chromosomes do not cause infertility, speculations concerning modes of speciation based on satellite DNA differences between otherwise homologous chromosomes would appear to be ill founded.

C-band polymorphism: comparison between trisomy 21 cases and mentally retarded controls

C-banding was done prospectively on 50 Down syndrome (trisomy 21) cases and 50 mentally retarded controls. Heterochromatin was quantitated by measuring the lengths of heterochromatin blocks and comparing these segments to the length of the short arm of chromosome 16 for 1, 9 and 16 heterochromatin, and to the total length of the Y chromosome for the Y heterochromatin in the distal long arm. For the first 30 individuals in each group, there was no difference in the mean lengths of C-band blocks of the 1, 9, 16 and Y chromosomes. For the total sample, there also was no difference between the trisomy 21 cases and controls in the number or size of pericentric inversions involving the heterochromatin blocks of chromosomes 1 and 9. Assuming random segregation of the parental C-band polymorphisms, this study gives no evidence for an association between such polymorphisms of the 1, 9, 16 and Y chromosomes and nondisjunction of chromosome 21.

Genes and non-coding DNA sequences

Many new categories of DNA sequence organization in higher organisms have been discovered in the last 20 years. Most of these are not found in bacterial and each in turn is hailed as a likely candidate for those regulatory elements which are assumed to distinguish higher from lower organisms. This article stresses the similarities between their sequence organizations and the continuing lack of convincing function for any of them. It suggests that these sequences often appear after chance recombinational events and their presence then facilitates further change. Within the constraints of proper function the genome is clearly able to find many organizational solutions of apparently equal advantage to the organism. Finally, an example of rapid genome reorganization resulting from selection for resistance to the drug methotrexate is considered.

Cytological studies of heterochromatin function in the Drosophila melanogaster male: autosomal meiotic paring

In Drosophila melanogaster it is now documented that the different satellite DNA sequences make up the majority of the centromeric heterochromatin of all chromosomes. The most popular hypothesis on this class of DNA is that satellite DNA itself is important to the pairing processes of chromosomes. Evidence in support of such a hypothesis is, however, circumstantial. This hypothesis has been evaluated by direct cytological examination of the meiotic behaviour of heterochromatically and/or euchromatically rear-ranged autosomes in the male. It was found that neither substantial deletions nor rearrangements of the autosomal heterochromatin cause any disruption of meiotic pairing. Autosomal pairing depends on homologs retaining sufficient euchromatic homology. This is the first clear demonstration that the highly repeated satellite DNA sequences in the heterochromatin of the second, third and fourth chromosomes are not important in meiotic pairing, but rather than some euchromatic homology in the autosome is essential to ensure a regular meiotic process. These results on the autosomes, when taken in conjunction with our previous studies on sex chromosome pairing, clearly indicate that satellite DNA is not crucial for male meiotic chromosome pairing of any member of the D. melanogaster genome.

Molecular cytogenetics of the Equidae. I. Purification and cytological localization of a (G + C)-rich satellite DNA from Equus przewalskii

A (G + C)-rich density satellite DNA (rho = 1.713 gm/cc) has been purified from splenic DNA of Przewalski's horse, Equus przewalskii, by successive equilibrium density gradient centrifugations. The purified satellite, which may comprise as much as 29% of the total DNA, renatures rapidly; however, analyses of native, single-stranded, and reassociated molecules by analytical ultracentrifugation and melting properties suggest that some sequence heterogeniety exists in the 1.713 gm/cc satellite. Complementary RNA (cRNA) transcribed from satellite DNA has been utilized for in situ hybridization studies with E. przewalskii metaphase chromosomes previously identified by quinacrine-banding. These studies establish that sequences complementary to the 1.713 g/cc satellite are greatly enriched in the centromeres of some, but not all, chromosomes. The differential distribution of satellite DNA sequences over heterochromatic regions allows discrimination of three classes of heterochromatin and serves to define three types of pericentromeric regions in the karyotype of this endangered equine species. Additionally, apparent polymorphism in concentrations of satellite DNA sequences between homologs in the same karyotype is noted.

Satellite DNA and heterochromatin variants: the case for unequal mitotic crossing over

Variations of constitutive heterochromatin (heteromorphisms) appear to be a general feature of eucaryotes. A variety of molecular and cytogenetic evidence supports the hypothesis that heteromorphisms result from unequal double-strand exchanges during mitotic DNA replication. Constitutive heterochromatin consists of highly repeated DNA sequences that are not transcribed. Thus, heteromorphisms are tolerated without overt phenotypic effect. Several of the highly repeated DNAs that comprise constitutive heterochromatin have been shown to contain site-specific endonuclease recognition sequences interspersed at regular intervals dependent upon nucleosome structure. These interspersed short repeated sequences could mediate unequal crossovers, resulting in quantitative variability of constitutive heterochromatin and satellite DNA. De novo variations of constitutive heterochromatin may be useful as markers of exposure to mutagens and/or carcinogens.

Specific arrangements of human satellite III DNA sequences in human chromosomes

DNA was extracted from various rodent-human somatic cell hybrids that contained single or a few human chromosomes. These DNAs were examined by a combination of restriction endonuclease digestion, gel electrophoresis, and filter hybridisation to radioactive satellite DNA probes following transfer of the denatured restriction fragments from a gel to a nitrocellulose filter. In this way the arrangement of sequences homologous to human satellite III were examined on human chromosomes 1, 7, 11, 15, 22 and X. It was found that the distribution of restriction endonuclease sites within satellite III DNA is different on different chromosomes.

The distribution of satellite and main-band DNA components in the melanogaster species subgroup of Drosophila. I. Fractionation of DNA in actinomycin D and distamycin A density gradients

Fractionation of total adult DNA of five of the seven species of the melanogaster species sub-group of Drosophila in actinomycin D and distamycin A caesium density gradients has revealed the presence of three main-band DNA components, common to all species, and ten satellite DNAs that are distributed between the species. Satellite DNAs are either unique to a species or common to two or more species. The abundance of a common satellite DNA varies between species. There is no simple relationship between the presence of a satellite DNA and a branch point of phylogenetic divergence; nevertheless the arrangement of the species in a phylogeny that is based on the numbers of satellites held in common accurately reflects the pattern of relationships between the same species based on differences in inversions of polytene chromosomes. The species can be similarly arranged according to the compositions of their mitochondrial DNAs. It is possible that the same basic set of sequences, each of low frequency, is common to all species with arbitrary or selected amplification of particular sequences to differing extents in individual species. The conservation of satellites in the group and the close parallel between the distributions of satellites and inversions between the species suggests that either the processes that operate to change both chromosomal phenomena are similarly time-dependent and occurring at relatively low rates or that their rates of change are restricted according to some undetermined functions of these aspects of the genome.

Conservation and chromosomal localization of DNA satellites in balenopterid whales

DNA satellites were isolated from three balenopterid species, viz. the minke, sei, and fine whales. In each of them at least two DNA satellites were recognizable with buoyant densities in neutral CsCl of rho = 1.702/1.703 and rho = 1.710/1;711, respectively. cRNAs from each satellite group were used for filter and in situ hybridisations. Homo-and heterologous DNA-cRNA hybrids within each satellite group yielded virtually identical melting curve profiles showing conservation of at least a considerable part of the DNA satellite sequences. There was no evident sequence homology between the rho = 1.702/1.703 and the rho = 1.710/1;711 satellites by filter hybridisation.--The in situ hybridisation showed that in each species the rho = 1.702/1.703 satellite was located in centromeric-paracentromeric C-bands in a few pairs, whereas the rho = 1.710/1.711 satellite was located in terminal C-bands throughout the karyotypes.--The data on the whale DNA satellites indicate that the quantitative evolution of the sateliite DNA sequences preceded species divergence of the balenopterids and that the satellite sequences have remained relatively unaltered since the divergence took place. The function of satellite DNA is considered to imply the introduction of both chromosomal and genic polymorphisms and thus being of great importance in speciation, Based upon these concepts a model is postulated for the function of satellite DNA. According to this model at meiotic pairing euchromatinheterochromatin overlapping between homologous chromosomes is considered to be of a general occurrence. This overlapping is presumed to be accentuated by the size heteromorphism frequently observed between homologous heterochromatic segments (C-bands). In the region of such euchromatinheterochromatin overlapping, cross-over would be excluded. The overlapping is suggested to be rectified progresssively in the chromosome arms, leaving unaffected crossing-over distant to the euchromatin-heterochromatin junctions. The consequence of this will be that genes in the proximity of the junctions are collectively inherited and selected, whereas genes distant to the the heterochromatin will be independently assorted and selected.

Genetic studies on heterochromatin in Drosophila melanogaster and their implications for the functions of satellite DNA

In Drosophila melanogaster the centromeric heterochromatin of all chromosomes consists almost entirely of several different satellite DNA sequences. In view of this we have examined by genetic means the meiotic consequences of X chromosomes with partial deletions of their heterochromatin, and have found that the amount and position of recombination on each heterochromatically deleted X is substantially different from that of a normal X. It appears that the amount of heterochromatin is important in modifying the "centromere effect" on recombination.--In all the deleted Xs tested, chromosome segregation is not appreciably altered from that of a nondeleted control chromosome. Thus satellite DNA does not appear to be an important factor in determining the regular segregation of sex chromosomes in Drosophila. Additionally, since X chromosomes with massive satellite DNA deficiencies are able to participate in a chromocenter within salivary gland nuclei, a major role of satellite DNA in chromocenter formation in this tissue is also quite unlikely.--In order to examine the mechanisms by which the amount of satellite DNA is increased or decreased in vivo, we have measured cytologically the frequency of spontaneous sister chromatid exchanges in a ring Y chromosome which is entirely heterochromatic and consists almost exclusively of satellite DNA. In larval neuroblast cells the frequency of spontaneous SCE in this Y is approximately 0.3% per cell division. Since there is no meiotic recombination in D. melanogaster males and since meiotic recombination in the female does not occur in heterochromatin, our results provide a minimum estimate of the in vivo frequency of SCE in C-banded heterochromatin (which is predominantly simple sequence DNA), without the usual complications of substituted base analogs, incorporated radioactive label or substantial genetic content.--We emphasise that: (a) satellite DNA is not implicated in any major way in recognition processes such as meiotic homologue recognition or chromocenter formation in salivaries, (b) there is likely to be continuous variation in the amount of satellite DNA between individuals of a species; and (c) the amount of satellite DNA can have a crucial functional role in the meiotic recombination system.