Dispersion Profiles and Gene Associations of Repetitive DNAs in the Euchromatin of the Beetle Tribolium castaneum.

Satellite DNAs are tandemly repeated sequences clustered within heterochromatin. However, in some cases, such as the major TCAST1 satellite DNA from the beetle Tribolium castaneum, they are found partially dispersed within euchromatin. Such organization together with transcriptional activity enables TCAST1 to modulate the activity of neighboring genes. In order to explore if other T. castaneum repetitive families have features that could provide them with a possible gene-modulatory role, we compare here the structure, organization, dispersion profiles, and transcription activity of 10 distinct TCAST repetitive families including TCAST1. The genome organization of TCAST families exhibit either satellite-like or transposon-like characteristics. In addition to heterochromatin localization, bioinformatic searches of the assembled genome have revealed dispersion of all families within euchromatin, preferentially in the form of single repeats. Dispersed TCAST repeats are mutually correlated in distribution and are grouped in distinct regions of euchromatin. The repeats are associated with genes, are enriched in introns relative to intergenic regions, and very rarely overlap exons. In spite of the different mechanisms of repeat proliferation, such as transposition and homologous recombination, all TCAST families share a similar frequency of spreading as well as dispersion and gene association profiles. Additionally, TCAST families are transcribed and their transcription is significantly activated by heat stress. A possibility that such common features of TCAST families might be related to their potential gene-modulatory role is discussed.

Satellite DNA as a driver of population divergence in the red flour beetle Tribolium castaneum.

Tandemly repeated satellite DNAs are among most rapidly evolving sequences in eukaryotic genome, usually differing significantly among closely related species. By inducing changes in heterochromatin and/or centromere, satellite DNAs are expected to drive population and species divergence. However, despite high evolutionary dynamics, divergence of satellite DNA profiles at the level of natural population which precedes and possibly triggers speciation process is not readily detected. Here, we characterize minor TCAST2 satellite DNA of the red flour beetle Tribolium castaneum and follow its dynamics among wild-type strains originating from diverse geographic locations. The investigation revealed presence of three distinct subfamilies of TCAST2 satellite DNA which differ in monomer size, genome organization, and subfamily specific mutations. Subfamilies Tcast2a and Tcast2b are tandemly arranged within pericentromeric heterochromatin whereas Tcast2c is preferentially dispersed within euchromatin of all chromosomes. Among strains, TCAST2 subfamilies are conserved in sequence but exhibit a significant content variability. This results in overrepresentation or almost complete absence of particular subfamily in some strains and enables discrimination between strains. It is proposed that homologous recombination, probably stimulated by environmental stress, is responsible for the emergence of TCAST2 satellite subfamilies, their copy number variation and dispersion within genome. The results represent the first evidence for the existence of population-specific satellite DNA profiles. Partial organization of TCAST2 satellite DNA in the form of single repeats dispersed within euchromatin additionally contributes to the genome divergence at the population level.

Satellite DNA-like elements associated with genes within euchromatin of the beetle Tribolium castaneum.

In the red flour beetle Tribolium castaneum the major TCAST satellite DNA accounts for 35% of the genome and encompasses the pericentromeric regions of all chromosomes. Because of the presence of transcriptional regulatory elements and transcriptional activity in these sequences, TCAST satellite DNAs also have been proposed to be modulators of gene expression within euchromatin. Here, we analyze the distribution of TCAST homologous repeats in T. castaneum euchromatin and study their association with genes as well as their potential gene regulatory role. We identified 68 arrays composed of TCAST-like elements distributed on all chromosomes. Based on sequence characteristics the arrays were composed of two types of TCAST-like elements. The first type consists of TCAST satellite-like elements in the form of partial monomers or tandemly arranged monomers, up to tetramers, whereas the second type consists of TCAST-like elements embedded with a complex unit that resembles a DNA transposon. TCAST-like elements were also found in the 5' untranslated region (UTR) of the CR1-3_TCa retrotransposon, and therefore retrotransposition may have contributed to their dispersion throughout the genome. No significant difference in the homogenization of dispersed TCAST-like elements was found either at the level of local arrays or chromosomes nor among different chromosomes. Of 68 TCAST-like elements, 29 were located within introns, with the remaining elements flanked by genes within a 262 to 404,270 nt range. TCAST-like elements are statistically overrepresented near genes with immunoglobulin-like domains attesting to their nonrandom distribution and a possible gene regulatory role.

Transcription of Satellite DNAs in Insects.

The very complex life cycle and extreme diversity of insect life forms require a carefully regulated network of biological processes to switch on and off the right genes at the right time. Chromatin condensation is an important regulatory mechanism of gene silencing as well as gene activation for the hundreds of functional protein genes harbored in heterochromatic regions of different insect species. Being the major heterochromatin constituents, satellite DNAs (satDNAs) serve important roles in heterochromatin regulation in insects in general. Their expression occurs in all developmental stages, being the highest during embryogenesis. satDNA transcripts range from small RNAs, corresponding in size to siRNAs, and piwiRNAs, to large, a few kb long RNAs. The long transcripts are preferentially nonpolyadenylated and remain in the nucleus. The actively regulated expression of satDNAs by cis or trans elements as well as by environmental stress, rather than constitutive transcription, speaks in favor of their involvement in differentiation, development, and environmental response.

A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages.

Macroevolutionary trends traditionally are studied by fossil analysis, comparative morphology or evo-devo approaches. With the availability of genome sequences and associated data from an increasing diversity of taxa, it is now possible to add an additional level of analysis: genomic phylostratigraphy. As an example of this approach, we use a phylogenetic framework and embryo expression data from Drosophila to show that grouping genes by their phylogenetic origin can uncover footprints of important adaptive events in evolution.