Family Of Repetitive Sequences Research Articles

Organization and chromosomal location of repetitive DNA sequences in three species of squamate reptiles

Repetitive DNA sequences were isolated from the genomes of species representing three major clades of squamate reptiles. A repetitive sequence (Cn4C7) was isolated from the New Mexican whiptail lizard, Cnemidophorus neomexicanus. This sequence is distributed throughout the chromosomes, but is more concentrated in the telomeric region. Cn4C7 also hybridizes to the chromosomes of other Cnemidophorus. Some evidence was found for concerted evolution of this repeat in hybrid unisexual lineages. In the lesser earless lizard, Holbrookia maculata, the predominant repeat in the genome is represented by a sequence (Hm1E11) which is restricted to the area flanking the centromere in all species of Holbrookia. Two families of repetitive sequences (one dispersed, and the other telomeric) were isolated from the western diamondback rattlesnake, Crotalus atrox. The type and distribution of repetitive sequences in squamates is often taxon-specific, and may be useful as characters for elucidating taxonomic relationships.

Amplification of DNA sequences in wheat and its relatives: the Dgas44 and R350 families of repetitive sequences.

The sequence of a Triticum tauschii genomic clone representing a family of D-genome amplified DNA sequences, designated Dgas44, is reported. The Dgas44 sequence occurs on all chromosomes of the D genome of wheat, Triticum aestivum, and in situ hybridization revealed it to be evenly dispersed on all seven chromosome pairs. An internal HindIII fragment of Dgas44, designated Dgas44-3, defines the highly amplified region that is specific to the D genome. The polymerase chain reaction was used to amplify a 236-bp fragment within Dgas44-3 from chromosomes 1D, 2D, 3D, 4D, 5D, and 7D, and identical copies of this region of the Dgas44-3 sequence were found among the isolates from each of the chromosomes. The Dgas44-3 sequence population from specific chromosomes differed on average by 0.22% from the original Dgas44 sequence. The Dgas44 sequence was found to differentiate between the D genome present in T. aestivum, T. tauschii, hexaploid T. crassum, T. cylindricum, T. ventricosum, in which the sequence was present in a highly amplified form and T. juvenale, T. syriacum, and tetraploid T. crassum where the sequence family was difficult to detect. Another class of amplified sequences previously considered to be rye "specific." R350, was isolated from tetraploid wheat and its dispersed distribution on chromosomes was similar to the Dgas44 family in T. tauschii. In contrast with the Dgas44 sequence family, genome specificity for the remnant R350 sequence family was not evident since it was present on all wheat chromosomes.

Discrimination of related transcribed and non-transcribed repetitive DNA sequences from the Y chromosomes of Drosophila hydei and Drosophila eohydei.

The short arm of the Y chromosome of Drosophila hydei carries a single male fertility gene, gene Q, which forms the lampbrush loop pair Nooses. Conflicting observations have been reported concerning the identity of the repetitive DNA sequences that are transcribed in this loop pair. It has been claimed by other investigators that the loop transcripts contain repeats of two distinct, but related families of Y-specific repetitive DNA sequences, ay1 and YsI. We reinvestigated this issue, using as probes single ay1 and YsI repeats which, under stringent conditions, hybridize only to members of their own family. Under non-stringent conditions, both repeats hybridize in situ to Nooses transcripts. However, if hybridization conditions are stringent, only the ay1 probe hybridizes to loop transcripts. Hybridizations to Northern blots of testis RNA confirm these results. Further, YsI repeats are not found the closely related species D. eohydei. We conclude that the YsI repeats are not relevant for the function of fertility gene Q.

Cloning and characterization of a fish centromeric satellite DNA.

A highly repetitive DNA sequence family from the genome of Sparus aurata has been cloned and characterized. The family is composed of repeat units of 186 bp in length, and it accounts for 2% of the fish genome. Data from Southern blots and in situ hybridization demonstrate that repeating units are tandemly arranged at the centromeres of all the chromosomes in this species. The repetitive sequence is AT rich (67%) and is characterized by short stretches of consecutive AT base pairs and by short direct and inverted repeats. Sequence analysis of six cloned monomers of the family reveals some variation among clones at random positions and also distinguishes two subfamilies of repeats that differ in a highly divergent block of 31 bp. These two subfamilies do not seem to be located in separate domains but occur together in the centromere of each chromosome pair. The presence of this repeat family in the genome of other Sparidae species, some of which are relatively distant from S. aurata, indicates that this repetitive sequence could be an important component of the centromere in this fish family.

Conventional protein coding genes in the Drosophila Y chromosome: is the puzzle of the fertility gene function solved?

Conventional protein coding genes in the Drosophila Y chromosome: is the puzzle of the fertility gene function solved?

Partial reconstruction of the lampbrush loop pair Nooses on the Y chromosome of Drosophila hydei.

We present the analysis of genomic DNA fragments that were isolated as potential segments of the lampbrush loop pair Nooses on the short arm of the Y chromosome of Drosophila hydei. More than 300 kb of DNA were recovered in BamHI lambda and cosmid clone groups. This DNA is composed of the Y-specific ay1 family of repetitive DNA sequences, and of other repetitive DNA sequences, which at least in part are also located elsewhere in the genome (Y-associated sequences). Two additional classes of DNA fragments were obtained from an EcoRI library. One of them consists of ay1 repeats without apparent interspersion, including a total of more than 300 kb of DNA. The other is composed of tandemly repeated YsI sequences, a Y-specific sequence derived from ay1. This class includes more than 400 kb of DNA, which is also not interspersed by other sequences. Our results show that only the ay1 repeats interspersed by Y-associated DNA sequences can represent parts of the 260 kb transcription unit forming the lampbrush loop, whereas the ay1 and YsI repeats without interspersion form separate and nontranscribed clusters of repetitive DNA.

Discovery by Minimal Length Encoding: A case study in molecular evolution

We apply the Minimal Length Encoding Principle to formalize inference about the evolution of macromolecular sequences. The Principle is shown to imply a combination of Weighted Parsimony and Compatibility methods that have long been used by biologists because of their good practical performance. The background assumptions are expressed as an encoding scheme for the observed data and as heuristic rules for selection of diagnostic positions in the sequences. The Principle was applied to discover new subfamilies of Alu sequences, the most numerous family of repetitive DNA sequences in the human genome.

Repetitive sequences in the genome of Anemone blanda: identification of tandem arrays and of dispersed repeats.

A tandemly repetitive sequence family (AbS1) and a repetitive sequence (Hd) forming part of a larger dispersed element (dorf-1) of Anemone blanda were characterised. The AbS1 satellite sequence family is located in all 4',6-diamidino-2-phenylindole (DAPI) positive intercalary heterochromatic bands and in the DAPI positive heterochromatic terminal region of chromosome 3, while the dispersed Hd homologous sequences are preferentially associated with euchromatic chromosome regions. The major component of the AbS1 satellite is AbS1-H1 with a basic repeat unit of 1640 bp; a minor fraction (AbS1-H5) consists of 320 bp units. A subsection of the AbS1-H1 repeat unit exhibits homologies to the 25S rRNA gene of flowering plants suggesting that the 1.64 kb satellite was generated by amplification of a precursor satellite and/or single copy sequence together with an rDNA fragment. The rDNA homologous region is considered to evolve at a rate similar to pseudogenes and thus the age of this satellite DNA fraction can be roughly estimated as about 27 million years. The dispersed repeated sequence Hd (about 1300 bp) is associated with the 8 kb element dorf-1. A. blanda dorf-1 constitutes about 0.2% of the genome (3 x 10(4) copies), is bounded by identical long terminal repeats, and exhibits partial homology to the Lilium gypsy-type element del1, but has yet to be confirmed as a retrotransposon. In contrast to the AbS1 satellite sequence family, Hd homologous sequences were found not only in A. apennina, the closest relative of A. blanda, but also in A. nemorosa and A. ranunculoides indicating that a progenitor sequence of dorf-1 was present in a common ancestor before speciation occurred.

Transposition of an Alu-containing element induced by DNA-advanced glycosylation endproducts.

Advanced glycosylation endproducts react with DNA and cause mutations and DNA transposition in bacteria. To investigate the mutagenic effect of advanced glycosylation in mammalian cells, plasmid DNA containing the lacI mutagenesis marker was modified by advanced glycosylation endproducts in vitro, transfected into murine lymphoid cells, recovered, and analyzed for mutations, plasmid size changes, and the presence of shared insertion sequences. An 853-bp host-derived DNA sequence, designated INS-1, was identified as an insertion element common to plasmids recovered from multiple independent transfections. Modification of DNA by advanced glycosylation increased by 60-fold the apparent frequency of INS-1 transposition: from 0.025% to 1.5%. The INS-1 element contains a 180-bp region that is homologous to the Alu repetitive sequence family. INS-1 was also observed to be present within larger insertional mutations and, in two cases, an apparently truncated version of INS-1 that lacks the Alu region was identified. These results demonstrate the experimental induction of DNA transposition involving mammalian chromosomal elements and suggest that advanced glycosylation may play a role in the formation of Alu-containing insertions that have been found to disrupt human genes.

Deletion Mapping and a Highly Reduced Radiation Hybrid in the Xp22.3-p22.2 Region

The human Xp22.3-p22.2 region contains several known disease genes as well as distinctive families of low copy repetitive sequences. In this study, we have developed new tools to more finely map this area. We have characterized a mapping panel of various cell lines and hybrids with different molecular breakpoints as defined by previously mapped reference markers from this region. The panel subdivides this area into nine distinct regions from DXS41 through the pseudoautosomal boundary. We have also identified a radiation-reduced somatic cell hybrid, Z4-7, that contains DXS31, DXS452, STS, DXS143, and DXS85, but not PABX, DXS16, or other single-copy probes from proximal Xp and Xq. A phage library was constructed from Z4-7 and over 80,000 plaques were screened with total human DNA. More than 100 positive clones were identified as potential new markers in this region. Nine of these have been mapped to the hybrid panel, and unique subclones have been isolated from three of these markers. The panel has also allowed us to map several other DNA markers, genes (AMG, OA1), and repetitive elements of the DXF22S and DXF30S sequence families relative to the various breakpoints.

Repetitive DNA sequence families in Crepis capillaris.

Three families of tandemly repetitive DNA from Crepis capillaris were cloned and characterized. Data obtained from in situ hybridization indicate that these families are located mainly in the heterochromatic C-bands. The pCcH32 family hybridizes at the paracentromeric C-band of the NOR (nucleolus-organized region) chromosome and along most of the long arm of the same chromosome. The pCcD29 family is located in all the remaining C-bands of the karyotype, while the third family, pCcE9, is restricted to the more proximal C-bands. Nucleotide sequence comparisons between one cloned repeating unit from each DNA family showed some significant regions of homology between the families. We discuss the sequence relationships between the three DNA families and the significance of our data in relation to models of heterochromatin evolution, emphasizing the concepts of equilocality and the differentiation of the NOR-bearing chromosome. We also examine the possible role that chromosome disposition, in either mitotic or meiotic nuclei, plays in the distribution and homogenization of heterochromatic DNA sequences.

Refined physical mapping of chromosome 16-specific low-abundance repetitive DNA sequences

Repetitive DNA sequences have been implicated in the origin of several disease phenotypes, including fragile X syndrome, myotonic dystrophy, and spinal bulbar atrophy. In addition, a complex family of chromosome 16-specific low-abundance repetitive (CH16LAR) DNA sequences have been mapped by fluorescence in situ hybridization to regions of chromosome 16 that undergo breakage/rearrangement in acute nonlymphocytic leukemia (ANLL) cells. It has been hypothesized that these repetitive sequences are causally related to the chromosome rearrangements found in ANLL. Here, we further refine the mapping of CH16LAR sequences with respect to the ANLL inversion breakpoints, using a panel of somatic cell hybrids containing 51 different chromosome 16 breakpoints. These studies indicate that CH16LAR sequences at 16p13 are in close proximity to the ANLL short-arm breakpoint region. However, the region containing the highest density of CH16LAR sequences on the long arm appears to be distal to the region where the ANLL long-arm breakpoint has been mapped. These studies further show that CH16LAR sequences map in close proximity to FRA16D and FRA16A.

Nucleotide sequences of BstUI repetitive elements from nuclear DNA of Chlorella ellipsoidea C-87

Abstract A ladder-like pattern of DNA fragments appeared when the nuclear DNA of Chlorella ellipsoidea C-87 was digested with Bst UI and separated by agarose gel electrophoresis. The DNA fragments of the ladder were cloned and sequenced, and were divided into two groups of repetitive sequence families whose members share a 15–16 by resemblant sequence (5′-GCCAAACGTCTCTGG-3′). These Bst UI repetitive sequences are strain-specific, but distributed through all 9 chromosomes of strain C-87.

Changes in chromatin structure due to hypomethylation induced with 5-azacytidine or DL-ethionine

Changes in chromatin structure of the HRS60 family of repetitive sequences in tobacco DNA were studied after hypomethylation induced with 5-azacytidine or DL-ethionine. The TaqI site in the HRS60 units lies in nucleosomal core regions and its cleavage is enhanced in the hypomethylated chromatin. In contrast, the cleavage of the Sau3A1 site located in linker DNA does not depend on the level of methylation of DNA.

Towards a physical map of the fertility genes on the heterochromatic Y chromosome of Drosophila hydei: families of repetitive sequences transcribed on the lampbrush loops Nooses and Threads are organized in extended clusters of several hundred kilobases.

The understanding of structure and function of the so-called fertility genes of Drosophila is very limited due to their unusual size--several megabases--and their location on the heterochromatic Y chromosome. Since mapping of these genes has mainly been done by classical cytogenetic analyses using a small number of cytologically visible lampbrush loops as the sole markers for particular fertility genes, the resolution of the genetic map of the Y chromosome is restricted to 3-5 Mb. Here we demonstrate that a substantially finer subdivision of the megabase-sized fertility genes in the subtelomeric regions of the Y chromosome of Drosophila hydei can be achieved by a combination of digestion with restriction enzymes having 6 bp recognition sequences, and pulsed field gel electrophoresis. The physical subdivision is based upon large conserved fragments of repetitive DNA in the size range from 50 up to 1600 kb and refers to the long-range organization of several families of repetitive DNA involved in Y chromosomal transcription processes in primary spermatocytes. We conclude from our results that at least five different families of repetitive DNA specifically transcribed on the lampbrush loops nooses and threads are organized as extended clusters of several hundred kb, essentially free of interspersed non-repetitive sequences.

Identification of two families of satellite-like repetitive DNA sequences from the zebrafish ( Brachydanio rerio)

To further our understanding of the structure and organization of the zebrafish genome, we have undertaken the analysis of highly and middle-repetitive DNA sequences. We have cloned and sequenced two families of tandemly repeated DNA fragments. The monomer units of the Type I satellite-like sequence are 186 bp long, A+T-rich (65%), and exhibit a high degree of sequence conservation. The Type I satellite-like sequence constitutes 8% of the zebrafish genome, or approximately 8 × 10 5 copies per haploid genome. Southern analysis of genomic DNA, digested with several restriction endonucleases, shows a ladder of hybridizing bands, consistent with a tandem array, and suggests longer range periodic variations in the sequence of the tandem repeats. The Type II satellite has a monomer length of 165 bp, is also A+T-rich (68%), and constitues 0.2% of the zebrafish genome (22,000 copies per haploid genome). Southern analysis reveals a complex pattern rather than a ladder of regularly spaced hybridizing bands.

The human THE-LTR(O) and MstII interspersed repeats are subfamilies of a single widely distributed highly variable repeat family

Fifteen examples of the transposon-like human element (THE) LTR and thirteen examples of the MstII interspersed repeat are aligned to generate new consensus sequences for these human repetitive elements. The consensus sequences of these elements are very similar, indicating that they compose subfamilies of a single human interspersed repetitive sequence family. Members of this highly polymorphic repeat family have been mapped to at least 11 chromosomes. Seven examples of the THE internal sequence are also aligned to generate a new consensus sequence for this element. Estimates of the abundance of this repetitive sequence family, derived from both hybridization analysis and frequency of occurrence in GenBank, indicate that THE-LTR Mst II sequences are present every 100–300 kb in human DNA. The widespread occurrence of members of this family makes them useful landmarks, like Alu, L1, and (GT) n repeats, for physical and genetic mapping of human DNA.

Attenuation in the rph-pyrE operon of Escherichia coli and processing of the dicistronic mRNA.

We have substituted on a plasmid the native promoter of the Escherichia coli rph-pyrE operon with an inducible transcription-initiation signal. The plasmid was used to study the mRNA chains derived from the operon at different intracellular concentrations of UTP and as a function of time following induction of transcription. The results showed that dicistronic rph-pyrE mRNA was formed when the UTP pool was low, and that a monocistronic rph mRNa was the major transcription product in high-UTP pools, thus supporting an UTP-controlled attenuation mechanism for regulation of pyrE gene expression. However, the dicistronic rph-pyrE transcript was rapidly processed into two monocistronic mRNA units, and a cleavage site was mapped near the attenuator in the intercistronic region, close to the site where transcription was terminated in high-UTP pools. Furthermore, the major 3' end of the pyrE mRNA was mapped near a palindromic structure of similarity to the family of repetitive extragenic palindromic sequences, 35 nucleotide residues after stop codon of the pryE gene.

Integration of bovine papillomavirus type 1 DNA and analysis of the amplified virus-cell junctions in transformed primary mouse fibroblasts.

We have analysed the site of bovine papillomavirus type 1 (BPV-1) DNA integration in clones originating from a transformed primary mouse fibroblast cell line established by transfection of linear BPV-1 DNA. Viral DNA was integrated at a single site in the host genome with an intact early region and an almost complete long control region. Sequence analysis showed that the BPV-1 DNA was integrated at the HindIII site (the enzyme used to linearize the BPV-1 DNA for transfection) with short deletions at both ends. These deletions correspond to a 534 bp segment spanning the 3' end of the L1 open reading frame and the replication enhancer element in the BPV-1 genome. The cellular sequences 5' to the viral integration site exhibited 85 to 97% identity to several sequences belonging to the mouse L1 family of long interspersed repetitive sequences. Cellular sequences 3' to the viral DNA exhibited no significant similarity to any known sequence. The BPV-1 sequences and the cellular flanking sequences were found to be amplified 45- to 50-fold. All the cell clones shared an identical integration site but one of the clones had an additional population of amplified and integrated BPV-1 DNA molecules with an internal deletion of 1136 bp in the late region. The significance of viral DNA integration at a murine long interspersed repetitive sequence containing an amplification-promoting sequence is discussed.

A micronucleus-limited sequence family in Tetrahymena thermophila: organization and sequence conservation.

During macronuclear development in the ciliated protozoan Tetrahymena thermophila, sequence reorganization including sequence loss occurs. Addressing questions about the organization and nucleotide sequence of micronucleus limited regions can lead to insights about mechanisms of DNA rearrangements during macronuclear development as well as mechanisms for the maintenance of the stability of micronucleus-limited sequence families. We have previously identified a moderately repetitive micronucleus-limited sequence family called X-H (family members hybridize to an approximately 450 bp Xbal-HindIII restriction fragment), completely absent from macronuclear DNA. The first member of this family which we isolated is associated with terminal sequences characteristic of a Tel-1 element, a putative micronuclear transposable element. Two additional family members have been isolated which are not closely associated with Tel-1 terminal sequences. We have nucleotide sequence data for three cloned members of the X-H family. This analysis has demonstrated that the longest cloned members of the X-H family share a region of homology of approximately 2,400 bp and are highly conserved, differing only by small insertions or deletions of 100 bp or less. The sequences from one of the sequenced family members flanking the region of homology are themselves mostly micronucleus-limited.