GSE132756
Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells
Heterochromatin protein 1a (HP1a) is a well-known component of pericentromeric and telomeric heterochromatin in Drosophila. However, its role and the mechanisms of its binding in the chromosome arms (ChAs) remain largely unclear. Here, we identified HP1a-interacting domains in the somatic cells of Drosophila ovaries using a DamIDseq approach and compared them with insertion sites of transposable elements (TEs) revealed by genome sequencing. Although HP1a domains cover only 13% of ChAs, they non-randomly associate with 42% of TE insertions. Furthermore, HP1a propagates from TE insertions at distances up to 10-kb. These data confirm the role of TEs in formation of HP1a islands in ChAs. However, only 18% of HP1a domains have adjacent TEs, indicating the existence of other mechanisms of HP1a domain formation besides spreading from TEs. In particular, many TE-independent HP1a domains correspond to the regions attached to the nuclear pore complexes (NPCs), or contain active gene promoters. Surprisingly, HP1a occupancy on the promoters of these genes does not lead to their repression. However, the steady-state transcript level of many genes located outside of HP1a domains was altered upon HP1a knockdown in the somatic cells of ovaries, thus pointing to the strong indirect effect of HP1a depletion. Collectively, our results support an existence of at least three different mechanisms of HP1a domain emergence in ChAs: spreading from TE insertions, interaction with the chromatin located near NPCs and targeting to the promoters of moderately expressed genes. Overall design: Amplified PCR fragments from DamID procedure were sequenced on Illumina HiSeq 2500, cDNA libraries were sequenced on Illumina HiSeq 1500.