Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes

How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer)-based fluorescence lifetime imaging microscopy (FLIM) approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells. Using RNAi and repetitive extrachromosomal array approaches, we defined the heterochromatin state and showed that its architecture presents a nanoscale-compacted organization controlled by Heterochromatin Protein-1 (HP1) and SETDB1 H3-lysine-9 methyltransferase homologs in vivo. Next, we functionally explored condensin complexes. We found that condensin I and condensin II are essential for heterochromatin compaction and that condensin I additionally controls lowly compacted regions. Our data show that, in living animals, nanoscale chromatin compaction is controlled not only by histone modifiers and readers but also by condensin complexes. [Display omitted] •Meiotic chromosomes in living C. elegans display heterogeneous nanoscale compaction•Heterochromatin has a compacted nanoscale organization controlled by HP1 and SETDB1 homologs•Tandem repeat-enriched ectopic chromosomes acquire heterochromatic structure in meiotic cells•Condensin I and II play essential roles in meiotic heterochromatin compaction How chromatin is structured in cells of living organisms remains poorly understood. Llères et al. adapted a FRET-based microscopic approach to monitor nanoscale chromatin compaction in the germline of living C. elegans. The study indicates heterogeneous compaction levels along pachytene chromosomes and reveals key roles of HP1 and condensin complexes.