Context-dependent effects of HP1 assessed in high throughput

Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporter genes (Akhtar, Cell, 2013; PMID: 23953119) with Gal4-mediated tethering of the protein of interest. We applied the assay to Drosophila Heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein working by a chromatin compaction mechanism but has also been linked to transcriptional activation. Probing the effects of HP1a in more than one thousand genomic locations revealed that HP1a is a potent repressor able to silence even highly expressing loci. However, the local chromatin context can modulate HP1a function. In pericentromeric regions, HP1a-induced repression was enhanced by two-fold. In regions marked by a H3K36me3-rich chromatin signature linked to transcriptional elongation, HP1a-dependent silencing was significantly decreased. We found no evidence for an activating function of HP1a in our experimental system. Furthermore, we did not observe stable transmission of repression over mitotic divisions after loss of targeted HP1a recruitment in any of the loci examined. The multiplexed tethered reporter assay will be a useful tool to dissect combinatorial regulatory interactions in chromatin. Overall design: TRIP assay in drosophila Kc167 cells combined with targeted recruitment of Gal4-HP1 to integrated 5xGa4UAS-pMT-GFP reporters. Two technical replicate experiments of TRIP pool transfected with Gal4-HP1, Gal4 or HP1 performed by day 2 and day 16 after transient transfection.