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

Abstract

Abstract 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.