Polymorphic curvature of satellite DNA in three subspecies of the beetle Pimelia sparsa

Sequence, Chromatin and Evolution of Satellite DNA

Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.

Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny

Simple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through nonallelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly. However, limited sampling has prevented detailed understanding of their evolutionary dynamics. Here, we characterize simple satellites from whole-genome sequences generated from males and females of nine Drosophila species, spanning 40 Ma of evolution. We show that PCR-free library preparation and postsequencing GC-correction better capture satellite quantities than conventional methods. We find that over half of the 207 simple satellites identified are species-specific, consistent with previous descriptions of their rapid evolution. Based on a maximum parsimony framework, we determined that most interspecific differences are due to lineage-specific gains. Simple satellites gained within a species are typically a single mutation away from abundant existing satellites, suggesting that they likely emerge from existing satellites, especially in the genomes of satellite-rich species. Interestingly, unlike most of the other lineages which experience various degrees of gains, the lineage leading up to the satellite-poor D. pseudoobscura and D. persimilis appears to be recalcitrant to gains, providing a counterpoint to the notion that simple satellites are universally rapidly evolving.

Characterization of two unrelated satellite DNA families in the Colorado potato beetle Leptinotarsa decemlineata (Coleoptera, Chrysomelidae)

The Colorado potato beetle (Leptinotarsa decemlineata, family Chrysomelidae),a phytophagous insect, which feeds preferably on potatoes, constitutes a serious pest of this crop and causes extensive damage to tomatoes and egg plants. It has a remarkable ability to develop resistance quickly against insecticides and shows a diversified and flexible life history. Consequently, the control of this pest has become difficult, requiring the development of new alternative biotechnology-based strategies. Such strategies require a thorough knowledge of the beetle’s genome,including the repetitive DNA. Satellite DNA (stDNA), composed of long arrays of tandemly arranged repeat units, constitutes the major component of heterochromatin and is located mainly in centromeric and telomeric chromosomal regions. We have studied two different unrelated satellite-DNA families of which the consensus sequences were 295 and 109bp in length, named LEDE-I and LEDE-II, respectively.Both were AT-rich (70.8% and 71.6%, respectively). Predictive models of sequence-dependent DNA bending and the study of electrophoretic mobility on non-denaturing polyacrylamide gels have shown that the DNA was curved in both satellite-DNA families. Among other features, the chromosome localization of both stDNAs has been studied. In situ hybridization performed on meiotic and mitoticnuclei showed chromosomes, including the X chromosome, with zero, one, or two stDNAs. In recent years, it has been proposed that the repetitive DNA may play a key role in biological diversification processes. This is the first molecular and cytogenetic study conducted on L. decemlineata repetitive DNA and specifically on stDNA, which is one of the important constituents of eukaryotic genomes.

Satellite DNA in insects: a review

The study of insect satellite DNAs (satDNAs) indicates the evolutionary conservation of certain features despite their sequence heterogeneity. Such features can include total length, monomer length, motifs, particular regions and/or secondary and tertiary structures. satDNAs may act as protein-binding sites, structural domains or sites for epigenetic modifications. The selective constraints in the evolution of satDNAs may be due to the satDNA sequence interaction with specific proteins important in heterochromatin formation and possible a role in controlling gene expression. The transcription of satDNA has been described in vertebrates, invertebrates and plants. In insects, differential satDNA expression has been observed in different cells, developmental stages, sex and caste of the individuals. These transcription differences may suggest their involvement in gene-regulation processes. In addition, the satDNA or its transcripts appear to be involved in heterochromatin formation and in chromatin-elimination processes. The importance of transposable elements to insect satDNA is shown by their presence as a constituent of satDNA in several species of insects (including possible active elements). In addition, they may be involved in the formation of centromeres and telomeres and in the homogenization and expansion of satDNA.

Structural and transcriptional features of Bombus terrestris satellite DNA and their potential involvement in the differentiation process

A unique satellite DNA family was characterized in the genome of the bumble bee, Bombus terrestris. Sequence analysis revealed that it contains two wide palindromes of about 160 and 190 bp, respectively, that span 75% of the repeated unit. One feature of this satellite DNA is that it accounts for different amounts of genomic DNA in males and females. The DNA curvature and bendability were determined by migration on PAGE and by computer analysis. It has been correlated with the presence of dA/dT stretches repeated in phase with the helix turn and with the presence of the deformable dinucleotide CA-TG embedded in some of these A-T-rich regions. Transcription of the satellite DNA was also analyzed by Northern blot hybridization and RT-PCR. Multimeric transcripts spanning several satellite DNA units were found in RNA samples from males, workers, and queens. These transcripts resulted from a specific transcription occurring on one DNA strand in the embryos or on both DNA strands in imagoes. The involvement of DNA curvature in the organization of the satellite DNA and the function of the satellite transcripts is discussed.

Complex structural features of satellite DNA sequences in the genus Pimelia (Coleoptera: Tenebrionidae): random differential amplification from a common 'satellite DNA library'

The major satellites of the nine species of the subgenera Pimelia s. str. and Amblyptera characterised in this paper are composed of longer monomers (500 and 700 bp) than those described previously in 26 Pimelia s. str. taxa (357 bp, a sequence called PIM357). Sequence analysis reveals partial similarity among these satellites and with the PIM357 monomers. The discrepancy between the phylogeny obtained based on three mitochondrial and two nuclear markers and that deduced from satellite DNA (stDNA) sequences suggests that the different Pimelia satellites were already present in a common ancestor forming what has been called a 'satellite DNA library'. Thus, the satellite profiles in the living species result from a random amplification of sequences from that 'library' during diversification of the species. However, species-specific turnover in the sequences has occurred at different rates. They have included abrupt replacements, a gradual divergence and, in other cases, no apparent change in sequence composition over a considerable evolutionary time. The results also suggest a common evolutionary origin of all these Pimelia satellite sequences, involving several rearrangements. We propose that the repeat unit of about 500 bp has originated from the insertion of a DNA fragment of 141 bp into the PIM357 unit. The 705-bp repeats have originated from a 32-bp direct duplication and the insertion of a 141-bp fragment in inverted orientation relative to a basic structure of 533 bp.

Structure-specific DNA-binding proteins as the foundation for three-dimensional chromatin organization

Any functions of tandem repetitive sequences need proteins that specifically bind to them. Telomere-binding TRF2/MTBP attaches telomeres to the nuclear envelope in interphase due to its rod-domain-like motif. Interphase nuclei organized as a number of sponge-like ruffly round chromosome territories that could be rotated from outside. SAF-A/hnRNP-U and p68-helicase are proteins suitable to do that. Their location in the interchromosome territory space, ATPase domains, and the ability to be bound by satellite DNAs (satDNA) make them part of the wires used to help chromosome territory rotates. In case of active transcription p68-helicase can be involved in the formation of local "gene expression matrices" and due to its satDNA-binding specificity cause the rearrangement of the local chromosome territory. The marks of chromatin rearrangement, which have to be heritable, could be provided by SAF-A/hnRNP-U. During telophase unfolding the proper chromatin arrangement is restored according to these marks. The structural specificity of both proteins to the satDNAs provides a regulative but relatively stable mode of binding. The structural specificity of protein binding could help to find the "magic" centromeric sequence. With future investigations of proteins with the structural specificity of binding during early embryogenesis, when heterochromatin formation goes on, the molecular mechanisms of the "gene gating" hypothesis (Blobel, 1985) will be confirmed.

Evolutionary dynamics of a satellite DNA in the tiger beetle species pair Cicindela campestris and C. maroccana

Satellite repeat elements are an abundant component of eukaryotic genomes, but not enough is known about their evolutionary dynamics and their involvement in karyotype and species differentiation. We report the nucleotide sequence, chromosomal localization, and evolutionary dynamics of a repetitive DNA element of the tiger beetle species pair Cicindela maroccana and Cicindela campestris. The element was detected after restriction digest of C. maroccana total genomic DNA with EcoRI as a single band and its multimers on agarose gels. Cloning and sequencing of several isolates revealed a consensus sequence of 383 bp with no internal repeat structure and no detectable similarity to any entry in GenBank. Hybridization of the satellite unit to C. maroccana mitotic and meiotic chromosomes revealed the presence of this repetitive DNA in the centromeres of all chromosomes except the Y chromosome, which exhibited only a very weak signal in its short arm. PCR-based tests for this satellite in related species revealed its presence in the sister species C. campestris, but not in other closely related species. Phylogenetic analysis of PCR products revealed well-supported clades that generally separate copies from each species. Because both species exhibit the multiple X chromosome karyotypic system common to Cicindela, but differ in their X chromosome numbers (four in C. maroccana vs. three in C. campestris), structural differences could also be investigated with regard to the position of satellites in a newly arisen X chromosome. We find the satellite in a centromeric position in all X chromosomes of C. maroccana, suggesting that the origin of the additional X chromosome involves multiple karyotypic rearrangements.

Evolutionary dynamics of satellite DNA family PIM357 in species of the genus Pimelia (Tenebrionidae, Coleoptera)

A large number of repeats of a satellite DNA (stDNA) family have been cloned and sequenced from species and populations of the genus Pimelia (Tenebrionidae, Coleoptera). The beetles were collected in the Canary Islands, Morocco, the Iberian Peninsula, and the Balearic Islands in order to analyze the evolutionary forces and processes acting on abundant stDNAs conserved at the genus level. This repetitive family is composed of an abundant A-T-rich stDNA, with basic units of 357 bp. All the sequences obtained showed similarity to the 22 repeat units of the PIM357 stDNA family described previously for six Iberian Pimelia species (Pons et al. 1997 ). An analysis based on similarity shows the presence of three different groups of sequences clearly in accordance with their geographical origin. One is composed of satellite sequences from Iberian and Balearic species, a second group from the Moroccan taxa, whereas the third one is from the Pimelia species endemic to the Canary Islands. The latter group shows higher nucleotide diversities for their stDNA sequences and a lack of relationship between transition stages to fixation and sequence divergence. Phylogeographic data of Canarian Pimelia show that the PIM357 stDNA family has persisted for more than 8 Myr and could probably be traced to the origin of the lineage. The data suggest that distinct demographic and phylogenetic patterns related to the colonization of the volcanic Canarian island chain account for particular evolutionary dynamics of the repeat DNA family in this group.

Occurrence of DNA sequences specifically recognized by drugs in human promoters

Several DNA-binding drugs are being developed to create tailored molecules which can discriminate among the different sequences of the whole genome. By discriminating among specific sites in DNA, these molecules may provide optimal drug therapy. The complete sequencing of the human genome offers a wealth of DNA targets to be analyzed as potential drug-binding sites. To increase our understanding of DNA-drug interactions and their selectivity, we have studied the relative and absolute occurrence of CG-rich sequences, of various lengths, in human gene promoters. In several promoters, including those of oncogenes, cell cycle regulation factors, tumor suppressors and housekeeping genes, the presence of potential binding sites containing CpG steps (in which many drugs are known to intercalate) is variable, but in many cases these sites are not randomly distributed. Sequences 6-7 base pairs in length, like CGCCCG or CGCCCCG, occur only once in some promoters, thus they may be potentially specific therapeutic targets.

Specificity of SAF-A and lamin B binding in vitro correlates with the satellite DNA bending state

There is evidence that Matrix Attachment Region (MAR)-binding proteins also bind satellite DNA (satDNA). The aim of the current work was to determine whether the major nuclear matrix (NM) MAR-binding proteins are able to recognize satDNAs of different locations and what DNA structural features are important for the recognition. In nuclei and NM, a number of the same polypeptides were recognized on a southwestern blot when MAR of immunoglobulin kappa gene (Ig kappa MAR) and pericentromeric (periCEN) satDNA fragments were used. However, the binding decreased dramatically when human and mouse CEN satDNA were used for the probes. After an NM extract was subjected to ion exchange chromatography, the main DNA-binding proteins were identified as SAF-A (scaffold attachment factor A) and lamin B. It was not possible to test the binding of lamin B by gel mobility shift assay (GMSA), but SAF-A showed an ability to distinguish CEN and periCEN satDNA fragments in GMSA. While periCEN fragments have an abnormally slow mobility on electrophoresis, which is a hallmark of bent DNA, CEN satDNA fragments have a normal mobility. A computer analysis was done using the wedge model (Ulanovsky and Trifonov [1987] Nature 326:720-722), which describes how the curved state depends on particular nucleotide sequences. The curved states of the fragments predicted by the model are in good agreement with their ability to be recognized by NM proteins. Thus SAF-A and lamin B are able to recognize conserved structural features of satDNA in the same way that MAR-binding proteins recognize MARs in spite of a lack of a consensus sequence. CEN and periCEN satDNAs are distinguished by proteins in correlation with the helical curvature of these fragments.

Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA

Satellite DNA sequences are known to be important components required for the construction of centromeres and are common to all higher eukaryotes. Nevertheless, their nucleotide sequences vary significantly, even in evolutionarily related species. In order to elucidate how the nucleotide sequences define the conformational character of centromeric satellite DNA, an evolutionary path toward repetitive units has been hypothesized. In that context, the DNA conformation of fish satellite DNA was evaluated in two ways: the organization of subrepeats and sequence characteristics were compared, and the differences in stacking energies between A-helix and B-helix and the sequence-dependent bendability of the helices were evaluated. Our findings suggest that the monomeric units making up currently observed repetitive sequences have evolved through stepwise amplification of shorter, ancestral sequences by increasing the length of the units. In addition, we suggest that potentially key sequences required for DNA amplification comprise highly flexible structures. Thus flexibility of the DNA structure may be a primary prerequisite for DNA amplification.

Satellite DNA in the ant Messor structor (Hymenoptera, Formicidae)

This paper is the first record of the satellite DNA of Formicidae. The satellite DNA of the ant Messor structor is organized in a tandem repeat of monomers of 79 bp. Like satellite DNAs of other insects, it is AT rich and presents direct and inverted internal repeats. Restriction analysis of the total DNA with methylation-sensitive enzymes strongly suggests that this DNA is undermethylated. The presence of this repetitive DNA in other species of the genus Messor is also tested.

A theoretical perusal of the satellite DNA curvature in tenebrionid beetles

The curvature patterns of seven satellite DNAs taken from beetles belonging to the family Tenebrionidae (Coleoptera) were modelled utilising a number of computer programs that describe and plot the curvature profiles of DNA. The theoretical analysis agreed with the experimentally observed curvature of most of these satellite DNAs, and its absence in Tribolium freemani and Tenebrio obscurus satellite I. In many cases, the tenebrionid satellite DNAs lack periodically repeated runs of phased-A-tracts, yet they represent a clear example of curved DNA. The macroscopic curvature of satellites from these closely related organisms confirmed that other sequence elements must be participating in the bending of these DNAs. Our modelling approaches are discussed, together with previous experimental results, in terms of the role played by DNA curvature in the organisation of satellite DNA and the tight compacting of heterochromatin.

DNA curvature in solution measured by fluorescence resonance energy transfer

The sequence-induced curvature of DNA fragments free in solution was characterized by measurements of the end-to-end distance using fluorescence resonance energy transfer (FRET). The 31 bp oligonucleotides were labeled at their 5' ends with fluorescein as the donor and rhodamine X as the acceptor. We compared a curved oligonucleotide with three phased A6 blocks and a control containing (AT)3 instead of the A6 blocks. The increased efficiency of energy transfer of the A6-containing DNA indicates the existence of a permanent sequence-induced curvature, the magnitude of which is in good agreement with estimates from theoretical curvature predictions. Energy transfer efficiency and correspondingly curvature increases with NaCl concentration.

Conservation of satellite DNA in species of the genus Pimelia (Tenebrionidae, Coleoptera)

Satellite DNA has been characterized in six allopatric species from the genus Pimelia: P. interjecta, P. integra, P. variolosa and P. baetica, inhabiting Iberian Peninsula, and P. elevata and P. criba, endemic to Balearic Islands Ibiza and Mallorca, respectively. All species show the presence of a single satellite DNA of a basic monomer length of 357 bp and A+T content of 69%, comprising a considerable amount of the genome (39%-45%, corresponding to about 4.5 x 10(5) copies per haploid genome). The sequence analysis of 22 cloned repeats reveals very high intra- and interspecific sequence similarity. Phylogenetic analysis separates the satellite sequences into two clusters, each comprising clones from three species exclusively. Within the clusters, satellite clones are not grouped species-specifically, except those of P. integra where species-diagnostic nt substitutions are detected with a pattern that could be produced by gene conversion. Such high sequence conservation could be related to preservation of satellite DNA curvature, resulting in a higher order helical structure, proposed to act as a specific protein binding domain.