UpSET modulates open chromatin features at active transcribed genes. Hector Rincon-Arano, Jessica Halow, Jeffrey Delrow, Susan Parkhurst, Mark Groudine. Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA.

   Chromatin accessibility is one of the main structural features that distinguish transcribing genes from non-expressing genes. Interestingly, active promoter regions exhibit a more open chromatin structure than gene bodies, which is suggested to be consequence of the complex machinery and catalytic activities targeted to the transcriptional start site. The SET domain-containing protein UpSET is part of a Rpd3/Sin3 histone deacetylase complex associated with transcribing genes and lack of this protein results in female sterility. The recruitment of UpSET-containing complexes to active regions modulates histone acetylation of active promoter regions. To evaluate whether UpSET also modulates chromatin accessibility we developed an in situ M.SssI-based chromatin accessibility assay. Our results show that upSET germariums possess higher chromatin accessibility than wildtype. MNase I-based chromatin accessibility assays in RNAi-based UpSET knock down in Kc cells confirms higher chromatin accessibility around UpSET target genes. These results correlate with the ability of upSET mutants to increase Polycomb phenotypes, which are chromatin structure dependent. Unexpectedly, transcription of UpSET target genes is not disturbed; nonetheless off-target genes and repetitive sequences are up-regulated in upSET mutants and knock down cells. Accordingly, position effect variegation of transgene array, but not centromeric or telomeric, silencing is suppressed in upSET mutants suggesting a main functional role in euchromatic regions. In consequence, upSET mutant ovaries exhibit up-regulation of the Notch pathway, which affects cell lineage specification of polar cells. Altogether, our results suggest that UpSET is a key transcriptional modulator of open chromatin features to fine tune gene expression thereby avoiding spurious gene expression.