Abstract
Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of “silent” H3K9me3 and “active” H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats. The results show H3K9me3 enrichment at alpha repeats upon heat stress, which correlates with the dynamics of alpha satellite DNA transcription activation, while no change in H3K4me2/3 level is detected. Spreading of H3K9me3 up to 1–2 kb from the insertion sites of the euchromatic alpha repeats is detected, revealing the alpha repeats as modulators of local chromatin structure. In addition, expression of genes containing alpha repeats within introns as well as of genes closest to the intergenic alpha repeats is downregulated upon heat stress. Further studies are necessary to reveal the possible contribution of H3K9me3 enriched alpha repeats, in particular those located within introns, to the silencing of their associated genes.
Highlights
Satellite DNAs are tandemly repeated sequences assembled within constitutive heterochromatin at thecentromeric and subtelomeric regions [1]
The human reference genome GRCh38.hg38 was searched with the alignment program BLASTN version 2.3.1+ using as the query a dimer of human alphoid 171 bp repeat consensus sequence derived from 293 cloned monomers of wide-ranging chromosomal origins [26]
The analyses revealed preferential organization of alpha satellite DNA within clusters composed of tandemly arranged repeats and the largest clusters are located within centromeric and pericentromeric regions of all chromosomes
Summary
Satellite DNAs are tandemly repeated sequences assembled within constitutive heterochromatin at the (peri)centromeric and subtelomeric regions [1]. Some satellite DNAs are clustered within heterochromatin in the form of long arrays but are dispersed as short arrays within euchromatin, in the intronic and intergenic regions [2,3,4,5,6]. Satellite DNAs are preferentially embedded in constitutive heterochromatin which is considered transcriptionally inert, their transcription was reported in vertebrates, invertebrates, and plants [7]. Temperature-mediated heterochromatin disruption seems to be an epigenetic event which includes stress-response transcription factors involved in heterochromatin assembly. Heat stress activates heat shock transcription factor 1 (HSF1) which recruits major cellular acetyltransferases to pericentric heterochromatin leading to targeted hyperacetylation [10], facilitating the transcription of satellite III DNA [11,12].
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