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

Cloning of a major repeat DNA sequence from Pyura stolonifera

We have cloned a 147-bp Hind III fragment from a marine ascidian Pyura stolonifera. This sequence is arranged in tandem in arrays up to 20 kb in size and represents more than 5% of the total genomic DNA. The basic 147-bp unit was isolated from Hind III-digested genomic DNA and cloned into M13. Sequence analysis of seven clones revealed that the sequence is AT rich (75%) and can be separated from main band DNA by equilibrium density gradient centrifugation in the presence of the ligand dye Hoechst 33258. The sequence is highly conserved and is changed only by single base substitution mutations in the different clones. Use of this sequence as a probe demonstrated varying degrees of hybridization with DNA isolated from a wide range of other ascidians. Northern blot analysis revealed the presence of RNA hybridizing to the repeat in unfertilized eggs but transcription of this sequence was not evident in the adult organism.

Truncated repeated sequences generated by recombination in a specific region

Structural relationships within a family of long repeated DNA sequences have been determined by molecular cloning of individual family members. About half of the family members are truncated at one end. There is a short, tandemly repeating region flanked by direct repeats associated with truncation. Recombination in a region near the tandemly repeating segment has apparently generated much of the diversity in this family.

A small chromatin-associated RNA homologous to repetitive DNA sequences

The chromatins of rat liver and chicken reticulocytes contain a small RNA of identical length (29 nucleotides). This RNA species differs from the degradation products of nuclear RNA present in the chromatin in possessing a free 3'-hydroxyl terminus. It stays associated with chromatin and is not released from the nuclei during the extraction of nuclear ribonucleoprotein particles. This RNA species was purified from the third fraction of non-histone chromosomal proteins eluted from Sephadex G-200 (fraction 3 RNA). When fraction 3 RNA, isolated from rat liver, was used to screen a rat genomic library approximately 3% of the phage plaques hybridized with the RNA. DNA isolated from four randomly selected hybridizing phage clones hybridized with purified 29-nucleotide RNA demonstrating that the sequences present in the four clones represent those of the 29-nucleotide RNA species and not those of minor contaminants. Each of the four clones contained a different amount of sequences complementary to the RNA species 29-nucleotides-long and in each clone the DNA sequences homologous to this RNA were surrounded by different restriction sites. Hybridization of 3'-32P-labeled fraction 3 RNA with blots of total genomic DNA established that some sequences homologous to this RNA are dispersed in the DNA and others are present on one EcoRI restriction fragment, which is approximately 6000 base pairs long. Fraction 3 RNA is not a degradation product of ribosomal or transfer RNA, it is transcribed from middle repetitive DNA and probably originates by specific release during the formation and/or processing of high-molecular-weight transcripts. In normal liver cells its sequences are not released into the cytoplasm.

An abundant family of methylated repetitive sequences dominates the genome of Physarum polycephalum

A significant portion (20%) of the Physarum genome can be isolated as a HpaII-resistant, methylated fraction. Cloned DNA probes containing highly-repeated sequences derived from this fraction were used to define the pattern of structural organisation of homologous repeats in Physarum genomic DNA. It is shown that the probes detect an abundant, methylated family of sequences with an estimated genomic repetition frequency greater than 2100, derived from a large repeated element whose length exceeds 5.8kb. Sequences comprising the long repetitive element dominate the HpaII-resistant compartment and account for between 4-20% of the Physarum genome. Detailed restriction/hybridisation analysis of cloned DNA segments derived from this compartment shows that HpaII/MspI restriction sites within some copies of the long repeated sequence are probably deleted by mutation. Additionally, segments of the repeat are often found in different organisational patterns that represent scrambled versions of its basic structure, and which are presumed to have arisen as a result of recombinational rearrangement in situ in the Physarum genome. Preliminary experiments indicate that the sequences are transcribed and that the structural properties of the repeat bear some resemblance to those of transposable genetic elements defined in other eukaryotic species.

Sequence organisation in nuclear DNA from Physarum polycephalum. Arrangement of highly-repeated sequences

Recombinant plasmids containing highly repetitive Physarum DNA segments were identified by colony hybridisation using a radioactively-labelled total Physarum DNA probe. A large number of these clones also hybridised to a foldback DNA probe purified from Physarum nuclear DNA. The foldback DNA probe was characterised by reassociation kinetic analysis. About one-half of this component was shown to consist of highly repeated sequences with a kinetic complexity of 1100 bp and an average repetition frequency of 5200. Direct screening of 67 recombinant plasmids for foldback sequences using the electron microscope revealed that about one-half were located in segments of DNA containing highly repetitive sequences; the remainder were present in clones containing low-copy number repeated elements. Analysis of two DNA clones showed that they contained repetitive elements located in over half of all DNA segments containing highly repetitive DNA and that the foci containing these highly repetitive sequences had different sequence arrangements. The results are consistent with the hypothesis that the most highly repeated DNA sequence families in the Physarum genome are few in number and are clustered together in different arrangements in about one-sixth of the genome. Over one-half of the foldback DNA complement in the Physarum genome is derived from these segments of DNA.

Organization and evolution of repeated DNA sequences in closely related plant genomes

In common with many other eukaryotic species, the genomes of species in the genus Allium contain a high proportion of repeated DNA sequences, which may be implicated in the considerable differences in genome size that are seen between even very closely related species. The gross organization of repetitive sequences within the genome of Allium sativum and of some other related species has been investigated using DNA/DNA hybridization studies. Such studies show that there has been much modulation in the amounts of different repeated DNA families during the evolution of the genus Allium; these repetitive elements are interspersed in all species with sequences of low repetition. The organization and distribution of one particular repetitive family within the genus has been examined using a cloned hybridization probe. Hybridization of this probe to DNA from related genomes reveals that this element is present in all Allium species examined, but with large-scale modulation of its abundance, and some considerable changes in its sequence environment. The evolution of such genome-specific arrangements of common repetitive elements and the possible mechanisms by which they might be maintained are discussed.

Repetitive sequences scattered throughout the genome of Trypanosoma cruzi

A clone bank from Trypanosoma cruzi DNA was constructed in the plasmid vector pBR325 and screened with total labelled DNA from the same parasite. The experimental conditions used enable recombinant clones containing repetitive sequences to be detected. 2% of the clones gave a strong positive signal. Half of them carried mini-circle sequences but the other half contained repetitive sequences from the nuclear genome. 50% of all colonies showed up more weakly suggesting that half of the trypanosome DNA fragments carried few repetitive elements. One family of repeats, present in two clones from different genomic regions, hybridized with a broad range of nuclear DNA fragment sizes. Moreover, one of these clones had at least two kinds of elements with no common sequences. A third clone, detected under the same conditions, hybridized with distinct nuclear DNA bands. The number of copies estimated for the latter was much lower than the number of homologous sequences detected in nuclear DNA with the former two. This third recombinant plasmid proved useful to differentiate among closely related trypanosome stocks. Neither poly(A)+ or poly(A)- RNA, nor the 50 kilobase pair band corresponding to the satellite DNA already described in trypanosomes, contribute to the repeats present within these recombinant DNAs. Sequences with some degree of homology were found in the nuclear genome of T. brucei and Crithidia fasciculata.