How metazoan genomes are structured at the nanoscale in living cells and tissues remains largely unknown. In addition, it still remains difficult to explore chromatin in vivo, particularly at both nucleosomal array level and single cell definition. Here, we applied a quantitative FRET (Forster resonance energy transfer)-based fluorescence lifetime imaging microscopy (FLIM) approach to measure nanoscale chromatin compaction in living primary cells and also at the scale of an organism, Caenorhabditis elegans. By measuring FRET between fluorescently-tagged core H2B histones, we spatially visualized distinct chromosomal regions and quantified the different levels of chromatin structuration.
In C.elegans, we combined RNAi approach to specifically define the heterochromatin state and showed that its architecture presents a nanoscale-compacted organization controlled by HP1 and SETDB1 H3-lysine-9 methyl-transferase homologs in vivo. Furthermore, we found that condensin I and condensin II regulate differentially the heterochromatin compaction state.
Altogether, our experimental system offers the exciting prospect to explore the effects of genetic and environmental factors on nanoscale chromatin compaction in living cells and in whole organisms.