Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

Abstract

Nuclear periphery (NP) plays substantial role in chromatin organization. Heterochromatin at the NP is intermitted with active chromatin surrounding nuclear pore complexes (NPCs), however, details of the peripheral chromatin organization are missing. To discern the distributions of epigenetic marks at the NP of HeLa nuclei, we used structured illumination microscopy combined with a new MATLAB software tool for an automatic NP and NPC detection, measurements of fluorescent intensity and statistical analysis of measured data. Our results show that marks for both active and non-active chromatin associate differentially with NPCs. The incidence of heterochromatin marks such as H3K27me2 and H3K9me2 was significantly lower around NPCs. In contrast, the presence of marks of active chromatin H4K5Ac and H3K4me2 was only little decreased around the NPCs or not at all (H3K9Ac). Interestingly, histone demethylases LSD1 and KDM2a were enriched within the NPCs suggesting the presence of chromatin modifying mechanism at the NPCs. Inhibition of transcription resulted in larger drop in the distribution of H1, H3K9me2 and H3K23me2 which implies the role of transcription in the organization of heterochromatin at the NP.