Isolation of a species-specific satellite DNA with a novel CENP-B-like box from the North African rodent Lemniscomys barbarus

Identification and characterization of satellite DNAs in two-toed sloths of the genus Choloepus (Megalonychidae, Xenarthra)

Choloepus, the only extant genus of the Megalonychidae family, is composed of two living species of two-toed sloths: Choloepus didactylus and C. hoffmanni. In this work, we identified and characterized the main satellite DNAs (satDNAs) in the sequenced genomes of these two species. SATCHO1, the most abundant satDNA in both species, is composed of 117 bp tandem repeat sequences. The second most abundant satDNA, SATCHO2, is composed of ~ 2292 bp tandem repeats. Fluorescence in situ hybridization in C. hoffmanni revealed that both satDNAs are located in the centromeric regions of all chromosomes, except the X. In fact, these satDNAs present some centromeric characteristics in their sequences, such as dyad symmetries predicted to form secondary structures. PCR experiments indicated the presence of SATCHO1 sequences in two other Xenarthra species: the tree-toed sloth Bradypus variegatus and the anteater Myrmecophaga tridactyla. Nevertheless, SATCHO1 is present as large tandem arrays only in Choloepus species, thus likely representing a satDNA exclusively in this genus. Our results reveal interesting features of the satDNA landscape in Choloepus species with the potential to aid future phylogenetic studies in Xenarthra and mammalian genomes in general.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

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.

New types of mouse centromeric satellite DNAs

Genomic databases do not contain complete sequences of the centromeric regions. We created a pUC19-based library of DNA fragments from isolated chromocentres of interphase nuclei. In this library we have found major satellite (MaSat) and two new satellite sequences - MS3 and MS4. The computer analysis of MS3 and MS4 sequences by alignment, fragment curved state and search for MAR motifs in comparison with the mouse major and minor satellite (MiSat) DNA has shown them to be new satellite fragments. Southern blot of MS3 and MS4 with total DNA digested by restriction enzymes shows the ladder characteristic of satellite DNA. 2.2% of the total DNA consists of MS3, the monomer of which is 150 bp long. The MS4 monomer is 300 bp long and accounts for 1.6% of the total DNA. On metaphase chromosomes MS3 and MS4 are located at the centromeric region. FISH analysis of L929 nuclei during the cell cycle showed relative positions of MaSat, MiSat, MS3, and MS4. All mapped satDNA fragments except MaSat belong to the outer layer of the chromocentres in the G0/G1 phase. MS3 is likely to be involved in the centromere formation. The mouse genome contains at least four satDNA types: AT-rich (MaSat and MiSat), and CG-rich (MS3 and MS4).

Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species

The functional centromeres of rice (Oryza sativa, AA genome) chromosomes contain two key DNA components: the CRR centromeric retrotransposons and a 155-bp satellite repeat, CentO. However, several wild Oryza species lack the CentO repeat. We developed a chromatin immunoprecipitation-based technique to clone DNA fragments derived from chromatin containing the centromeric histone H3 variant CenH3. Chromatin immunoprecipitation cloning was carried out in the CentO-less species Oryza rhizomatis (CC genome) and Oryza brachyantha (FF genome). Three previously uncharacterized genome-specific satellite repeats, CentO-C1, CentO-C2, and CentO-F, were discovered in the centromeres of these two species. An 80-bp DNA region was found to be conserved in CentO-C1, CentO, and centromeric satellite repeats from maize and pearl millet, species which diverged from rice many millions of years ago. In contrast, the CentO-F repeat shows no sequence similarity to other centromeric repeats but has almost completely replaced other centromeric sequences in O. brachyantha, including the CRR-related sequences that normally constitute a significant fraction of the centromeric DNA in grass species.

Molecular characterization of the first satellite DNA with CENP-B and CDEIII motifs in the bat Pipistrellus kuhli

The centromere is an essential structure in the chromosomes of all eukariotes and is central to the mechanism that ensures proper segregation during mitosis and meiosis. The comparison of DNA sequence motifs, organization and kinetocore components from yeast to man is beginning to indicate that, although centromeres are highly variable DNA elements, a conserved pattern of sequence arrangement and function is emerging. We have identified and characterized the first satellite DNA (P.k.SAT) from microbat species Pipistrellus kuhli. The presence of mammalian CENP-B box and yeast CDEIII box could indicate the participation of P.k.SAT in centromere organization.

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.

Pericentric satellite DNA sequences in Pipistrellus pipistrellus (Vespertilionidae; Chiroptera)

This paper reports the molecular and cytogenetic characterization of a HindIII family of satellite DNA in the bat species Pipistrellus pipistrellus. This satellite is organized in tandem repeats of 418 bp monomer units, and represents approximately 3% of the whole genome. The consensus sequence from five cloned monomer units has an A-T content of 62.20%. We have found differences in the ladder pattern of bands between two populations of the same species. These differences are probably because of the absence of the target sites for the HindIII enzyme in most monomer units of one population, but not in the other. Fluorescent in situ hybridization (FISH) localized the satellite DNA in the pericentromeric regions of all autosomes and the X chromosome, but it was absent from the Y chromosome. Digestion of genomic DNAs with HpaII and its isoschizomer MspI demonstrated that these repetitive DNA sequences are not methylated. Other bat species were tested for the presence of this repetitive DNA. It was absent in five Vespertilionidae and one Rhinolophidae species, indicating that it could be a species/genus specific, repetitive DNA family.

Comparative study of satellite DNA in ants of the Messor genus

The satellite DNA of ants Messor barbarus and Messor bouvieri is analysed. The results are compared with the satellite DNA data from Messor structor previously reported and with new data obtained from the genome of geographically distinct M. structor population, which have shown that this satellite DNA is highly conserved within the species. The satellite DNA is organized as tandemly repeated 79 bp monomers in all species. The sampled sequences of the three species show a high similarity and all belong to the same family of satellite DNA. Sequence comparisons suggested the occurrence of highly effective homogenization mechanism acting upon the ant genomes. In accordance with this hypothesis, putative gene conversion tracts are identified when the different monomers of the same species are compared. The highest sequence conservation in all species corresponds to a single region with inverted repeats. A CENP-B-like motif was found in this region. The possibility that it may be involved in the homogenization of satellite DNA is discussed.