A molecular description of telometic heterochromatin in secale species

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

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

Preferential C-banding of wheat or rye chromosomes

Using different stains, wheat chromosomes could be distinguished from rye chromosomes by preferential staining. C-bands of rye chromosomes were preferentially stained with Giemsa while those of wheat chromosomes were preferentially stained with either Leishman or Wright stain. Preferential staining aids the identification of wheat and rye chromosomes and chromosome segments and in particular the recognition of wheat/rye chromosome substitutions and translocations.

Structural variation in the heterochromatin of rye chromosomes in triticales

Although Giemsa C-banding techniques have been used extensively for assaying cereal heterochromatin, a more specific technique for analyzing cereal heterochromatin has been developed recently with the isolation of DNA sequences present in heterochromatin and their employment in in situ hybridization to cereal chromosomes. A number of triticales were examined for the occurrence of modified rye chromosomes using the in situ hybridization technique. With a heterogeneous sequence probe the amount of rye heterochromatin appears to be relatively constant in wheat backgrounds but when a specific sequence probe was employed variation was observed. Whether this variation reflects polymorphism in rye or whether it is a result of adaption of the rye genome to coexistence with the wheat genome in triticales is discussed. - The triticale Rosner was examined in detail and it was established that the rye chromosome 2R had been replaced by the wheat chromosome 2D.

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.

Organization of highly repetitive satellite DNA of two Cucurbitaceae species (Cucumis melo and Cucumis sativus)

The prominent satellites of the Cucurbitaceae Cucumis melo (melon) and Cucumis sativus (cucumber) have been characterized, in actinomycin/CsCl gradients where the satellite sequences can be separated from ribosomal, organelle, and main band DNA the location of the satellites is different indicating a different GC content. The purified satellite of C. melo is cut by HindIII into a repeat unit of 380 bp; AluI digestion gives rise to two bands (about 80 and 220 bp in size). The HindIII repeat unit if cloned into pBR325 exhibits new recognition sites for HpaII leaving two bands with 150 and 80 bp suggesting methylation of the C/CGG cutting site in the uncloned material. The restriction pattern indicates an internal sequence repeat within the 380 bp HindIII fragment. The C. sativus satellite is cut by AluI to a repeat unit of 180 bp showing no other recognition site for the restriction enzymes tested so far. About 10% sequence homology has been determined between the C. melo and C. sativus satellites by cross hybridization studies. A high methylation degree of cytosines has been measured for both satellites and the ribosomal DNA of C. sativus (about 30%). No transcription products of the C. melo satellite were found during seedling development.

THE RYE GENOME IN WINTER HEXAPLOID TRITICALES

In eight winter triticales (× Triticosecale Wittmack) chosen from the Cambridge crossing program all seven rye (Secale cereale L.) chromosomes were present. However, a number of rye chromosomes showed an obvious reduction in the size of C-bands at one or more telomeres, compared with normal rye. In two lines the C-band at the short arm telomere of 2R was obviously larger than normal in rye. Comparison of these results with those published for spring triticales suggests that divergent selection pressures may determine the number and structure of rye chromosomes in winter and spring lines. In particular it is suggested that the differences may represent environmental adaptation and reflect selection pressure on the rye genome in triticale to conform to the cline for DNA amount per diploid genome on latitude previously described in cereal grain crops.

Clustering and methylation of repeated DNA: persistence in avian development and evolution

In the chicken genome, clusters of repeated DNA sequences occur which have alternate arrangements of the component sequence elements. Many of these clustered, repeated sequences are extensively methylated. We have established that both their arrangement and their methylation are invariant regardless of the source of chicken DNA. Comparisons included DNA from sperm, from a series of embryonic stages, from tissues of single adult individuals, and from thirty individual chickens of two strains. These same sequences are found in the DNA of some avian species related to chickens, and there they show the same clustered, methylated form. In related species, some of the arrangements found in chicken DNA are different or missing.

Duplication/deletion polymorphism 5' - to the human beta globin gene

DNA sequence analysis of the human beta globin locus has identified an array of simple tandem repeated sequences upstream from the beta globin structural gene. Comparison of several cloned human beta globin alleles demonstrated a high frequency of sequence heteromorphism at this site apparently due to duplication or deletion of single units of the repeat array. At least two such duplication/deletion events are necessary to account for the observed variation. No other sequence variation was observed, suggesting that duplication/deletion events within the tandem repeat array may be at least 13 to 14 times more frequent than nucleotide substitutions in the surrounding DNA.

Inserted sequences in bovine satellite DNA's

The nucleotide sequence of the 1413-base-pair repeat unit of bovine 1.711a satellite DNA (density in cesium chloride, 1.711 grams per cubic centimeter) has been determined. The repeat unit contains two segments consisting of variants of a basic 23-base-pair sequence that is closely related to sequences of bovine 1.706 satellite DNA. A third segment of the repeat unit contains an unrelated 611-base-pair sequence that is not internally repetitive. This segment is flanked by inverted repeats of 8 base pairs and, on one side, by a direct repeat of the terminal sequence. A related segment is present in bovine 1.711b satellite DNA and is inserted into sequences derived from the 1.715 satellite. These nucleotide sequences suggest the timing of some of the stages in the evolution of these complex, closely related satellite DNA's and indicate the mechanisms inherent in their divergence from a common ancestor.

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

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

Repeated deoxyribonucleic acid clusters in the chicken genome contain homologous sequence elements in scrambled order

Part of the repeated deoxyribonucleic acid (DNA) in the chicken genome had a clustered organization. The following description of clustered repeated sequences is derived both from analysis of DNA segments cloned in lambda and from hybridization of individual cloned sequences to Southern blots of restricted total DNA. A cluster usually exceeds 20 kbp in length and consists principally, if not entirely, or repetitive DNA. Each cluster contains one cope of several different repeated sequences. The individual sequences occur several hundred times in the genome, but only once per cluster. Many of the clusters contain the same assortment of sequences but in scrambled order. In the genome, those repeated sequences that are elements of clusters occur mainly within the clustered context and are seldom, if ever, found as isolated elements flanked by nonrepeated DNA. These aspects of cluster organization suggest that the clustered sequences undergo limited rearrangement, maintaining the associations within clusters but allowing variability of sequence arrangement from cluster to cluster. The clusters that occupy the cloned DNA segments together represent at least 10% of the repetitive DNA of the chicken.

The DNA sequences of cloned complex satellite DNAs from Hawaiian Drosophila and their bearing on satellite DNA sequence conservation

A class of restriction endonuclease fragments near 185 bp in length and comprising approximately 20% of the genomes of 3 species of Hawaiian Drosophila has been cloned using bacteriophage M13. The nucleotide sequences of 14 clones have been determined and the variation between clones has been found to be due to deletions and base changes. Analyses of uncloned material show that the cloning system itself does not introduce the variation. The variation of the basic repeat within and between species is high; 15% due to deletions and 10% due to base changes. The Drosophila data are similar in many respects to both the 23 bp calf satellite results (Pech et al., 1979 b) and those from sequence analyses of the 170 bp primate restriction fragments (Rubin et al., 1979; Donehower et al., 1980, Wu and Manuelidis, 1980). The intraspecies level of base changes and deletions in the calf satellite approaches 25% as does that in the human/African green monkey/baboon comparisons. The between species variation in the primate group is near 35%. Direct sequencing methods thus reveal a widespread sequence heterogeneity in both invertebrate and mammalian satellite systems of long or short repeat length. This heterogeneity does not support the strict sequence conservation implied by the "library" hypothesis, which claims a functional role in speciation for the rigid conservation of satellite DNA sequences (Fry and Salser, 1977). Furthermore the Drosophila and primate data reveal that satellite DNAs can change rapidly, though nonrandomly, at the nucleotide sequence level in a relatively closely knit group such as the Hawaiian species, as well as in more distantly related species from amongst the primates. We draw two major conclusions. There is no universal attribute of satellite DNA sequence per se, the only biological variable to date being the amount of satellite DNA and its effect in the germ line. Many aspects of satellite DNA evolution conform to Kimura's (1979) concepts of neutrality.

Evolutionary sequence divergence within repeated DNA families of higher plant genomes. II. Analysis of thermal denaturation

An assay based on derivative analysis of thermal denaturation (melting) behavior of reassociated DNA was developed in an attempt to characterize the sequence relationships in repeated DNA families according to the homogeneous or heterogeneous models of Bendich and Anderson (1977). The validity of the technique was confirmed by the use of deaminated Escherichia coli DNA models for repetitive families. The melting data for DNA reassociated at two different temperatures provided strong evidence that Pisum sativum repeated families are mostly heterogeneous, while homogeneous families predominate in Vigna radiata. These findings, together with other differences between the two genomes, suggest that the rate of sequence amplification has been higher in the evolutionary history of Pisum DNA. A general trend seems to exist for high amplification rates in large, highly repetitive plant genomes such as Pisum and lower rates in smaller plant genomes such as Vigna, as well as in the generally smaller, less repetitive genomes of most animal species.

The distribution of repetitive DNAs between regular and supernumerary chromosomes in species of Glossina (Tsetse): a two-step process in the origin of supernumeraries

Several species of tsetse fly within the Morsitans and Fusca subgenera of Glossina contain supernumerary (B) chromosomes. Previous studies on the meiotic behaviour of chromosomes (Southern and Pell, 1973) and the C-band patterns (Jordan et al., 1977) have indicated a close similarity between the Y chromosome and the supernumeraries. The distributions of the highly abundant families of DNA (satellite DNAs) between the autosomes, sex chromosomes and B chromosomes of G.m. morsitans, G. austeni and G. pallidipes have been examined by in situ hybridisation. In addition, the organisation and sequence homologies of satellite DNAs have been examined by restriction enzymes and heterologous hybridisations in in situ and "Southern" transfer conditions. The majority of satellite sequences that are homologous between species are distributed in several different arrangements between A and B chromosome telomeres with minority sequences at some centromeric and intercalary locations. There is no extensive satellite DNA similarity between the Y and B chromosomes. We suggest that the Y and B chromosome associations and synchronous allocycly during meiosis are the result of extensive heterochromatinisation of these two chromosome types, that is probably a reflection of two separate stages involved in the generation of the B chromosomes in the genus. The independent evolution of satellites and supernumeraries is discussed.