Abstract
Non-coding repetitive DNAs have been proposed to perform a gene regulatory role, however for tandemly repeated satellite DNA no such role was defined until now. Here we provide the first evidence for a role of satellite DNA in the modulation of gene expression under specific environmental conditions. The major satellite DNA TCAST1 in the beetle Tribolium castaneum is preferentially located within pericentromeric heterochromatin but is also dispersed as single repeats or short arrays in the vicinity of protein-coding genes within euchromatin. Our results show enhanced suppression of activity of TCAST1-associated genes and slower recovery of their activity after long-term heat stress relative to the same genes without associated TCAST1 satellite DNA elements. The level of gene suppression is not influenced by the distance of TCAST1 elements from the associated genes up to 40 kb from the genes’ transcription start sites, but it does depend on the copy number of TCAST1 repeats within an element, being stronger for the higher number of copies. The enhanced gene suppression correlates with the enrichment of the repressive histone marks H3K9me2/3 at dispersed TCAST1 elements and their flanking regions as well as with increased expression of TCAST1 satellite DNA. The results reveal transient, RNAi based heterochromatin formation at dispersed TCAST1 repeats and their proximal regions as a mechanism responsible for enhanced silencing of TCAST1-associated genes. Differences in the pattern of distribution of TCAST1 elements contribute to gene expression diversity among T. castaneum strains after long-term heat stress and might have an impact on adaptation to different environmental conditions.
Highlights
Non-coding repetitive DNA includes diverse types of sequences which comprise a considerable portion of most eukaryotic genomes and their function is intensively investigated
We analyse a gene-regulatory role for tandemly repeated satellite DNA which is the major building element of pericentromeric and centromeric heterochromatin in many eukaryotes
Satellite DNA Modulates Gene Expression the beetle Tribolium castaneum which has a major satellite DNA preferentially located in pericentromeric heterochromatin but satellite repeats are dispersed in the vicinity of protein-coding genes within euchromatin
Summary
Non-coding repetitive DNA includes diverse types of sequences which comprise a considerable portion of most eukaryotic genomes and their function is intensively investigated. There are several examples of satellite DNAs present not exclusively within pericentromeric heterochromatin and dispersed as single repeats or short arrays in the vicinity of genes within euchromatin, such as the 1.688 Drosophila melanogaster satellite DNA [7] and two satellite DNAs from the beetle Tribolium castaneum [8,9]. Such dispersed organizational patterns might be formed due to intrastrand homologous recombination within satellite arrays [10], resulting in the formation of extrachromosomal circles [11] and their subsequent insertion throughout the genome [8,9]. Increasing evidence on the reorganization of heterochromatin elicited by heat stress and other stress treatments could indicate a possible role for satellite DNA in a general stress response activated in cells to cope with harmful conditions [4]
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