Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.
E-GEOD-47464 - Role of Fft3 in nuclear organization [DamID-chip, ChIP-chip]
Released on 2 March 2015, last updated on 7 March 2015
In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3Δ cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements at the borders of subtelomeres and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and components of the nuclear envelope by maintaining chromatin structure required for anchoring DNA insulators to nuclear pores. For DamID samples, we recorded methylation levels for Dam fusion proteins and compared them to Dam-only control samples. For ChIP samples, we compared immuno-precipitated DNA to mock or input controls.
ChIP-chip by tiling array, methylation profiling by array
Agata Smialowska, Annelie Strålfors, Babett Steglich, Jean P Javerzat, Jenna Persson, Karl Ekwall, Olga Khorosjutina