Satellite DNA in gene regulation and environmental adaptation (SatGenReg)
Repetitive elements can be a source of regulatory sequences and could act to distribute regulatory elements throughout the genome. In particular, mobile transposable elements are known to be a source of noncoding material that influences evolution of gene regulatory networks. Satellite DNAs are major building elements of pericentromeric and centromeric heterochromatin in many eukaryotes, and in certain species they account for the majority of genomic DNA. Wide evolutionary distribution, presence of functional elements such as promoters and transcription factor binding sites within some satellite DNA sequences as well as transcriptional activity of many satellites has led to the assumption that in addition to participating in centromere formation, they might also act as regulatory elements of gene expression. However, gene-regulatory role of satellite DNAs in not described till now. To perform potential regulatory function, satellite DNA elements are predicted to be preferentially distributed in euchromatic portion of the genomes, in the vicinity of genes. Whole genome sequencing projects enable the presence and distribution of satellite DNA repeats in the euchromatic portion of the genome to be determined.
In the red flour beetle Tribolium castaneum (Coleoptera) satellite DNAs, as the major heterochromatin constituents, play important role in heterochromatin regulation and remodelling during development and environmental stress response. Expression of a major satellite DNA TCAST1 is strongly induced by heat shock, and increased level of satellite-derived small interfering RNAs (siRNAs) is accompanied by increase of repressive epigenetic modifications of histones at satellite DNA regions. In addition to the presence in the heterochromatin, short stretches of satellite DNA have been mapped in the close vicinity of numerous genes within euchromatin. The environmentally susceptible transcription of TCAST1 satellite DNA from the internal promoters as well as distribution close to protein-coding genes provides strong support for its role in gene regulation and adaptation to different environmental conditions.
The aim of the proposed project is to investigate the gene-regulatory role of satellite DNAs in insect T. castaneum. We propose that satellite DNA-associated siRNAs could affect epigenetic state of euchromatic regions containing dispersed satellite elements by targeting these elements in a sequence-specific manner and by guiding chromatin modifiers, primarily histone methyltransferase. This could result in heterochromatin assembly at dispersed satellite DNA elements and its spreading to the flanking region. Such “heterochromatization” is expected to influence the expression of genes located in the vicinity, most probably by decreasing the level of gene expression.
We expect that our results will for the first time demonstrate role of satellite DNAs in the modulation of protein-gene expression and reveal the molecular mechanism of their gene-regulatory activity. Satellite DNAs comprise a significant portion of T. castaneum genome and study of their potential gene-regulatory role could give significant contribution to the understanding of the beetle's genome function. Since the satellite DNA repeats change more frequently than other stretches of DNA do, it can be proposed that such genomic setup allows the organism to evolve more quickly and to adapt to different environmental conditions. Understanding of molecular basis of adaptation, especially to the different thermal conditions as well as chemical environment, could be of significant importance for the control of Tribolium castaneum, an important pest of stored agricultural products.