Abstract
BackgroundTranscription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. The regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. Emerging evidence suggests that genome organization and transcriptional regulation are inter-linked. However, the pericentromeric genome organization is relatively less studied. Therefore, we sought to characterize the pericentromeric genome organization and understand how this organization along with the pericentromeric factors influences heterochromatic gene expression.ResultsHere, we characterized the pericentromeric genome organization in Drosophila melanogaster using 5C sequencing. Heterochromatic topologically associating domains (Het TADs) correlate with distinct epigenomic domains of active and repressed heterochromatic genes at the pericentromeres. These genes are known to depend on the heterochromatic landscape for their expression. However, HP1a or Su(var)3-9 RNAi has minimal effects on heterochromatic gene expression, despite causing significant changes in the global Het TAD organization. Probing further into this observation, we report the role of two other chromatin proteins enriched at the pericentromeres-dMES-4 and dADD1 in regulating the expression of a subset of heterochromatic genes.ConclusionsDistinct pericentromeric genome organization and chromatin landscapes maintained by the interplay of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) are sufficient to support heterochromatic gene expression despite the loss of global Het TAD structure. These findings open new avenues for future investigations into the mechanisms of heterochromatic gene expression.
Highlights
Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code
Pericentromeric heterochromatin is organized into distinct TADs To investigate the pericentromeric genome organization and its contribution to heterochromatic gene expression, we mapped the long-range DNA interactome in the Drosophila melanogaster pericentromeric heterochromatin (PCH)
Given the dearth of information regarding the hierarchical genome organization within the pericentromeres, our findings provide a detailed characterization of the Drosophila melanogaster PCH domains, which set the stage for further probing into its functional role in heterochromatic gene expression
Summary
Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. The abrogation of heterochromatic gene expression upon chromosomal translocation into the euchromatin [14,15,16], or the depletion of heterochromatic factors [17, 18], suggests that the genome organization and local concentration of certain heterochromatic trans factors might play a crucial role in their expression. These genes have been moved into the heterochromatin in the course of drosophilid evolution [19, 20]. The mechanisms by which they adapted to stay active in the repressive chromatin environment remains unclear
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