H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification

Gene silencing by chromatin compaction is integral to establishing and maintaining cell fates. H3K9me3-marked heterochromatin is reduced in embryonic stem cells compared to differentiated cells. However, the establishment and dynamics of closed regions of chromatin at protein coding genes, in embryologic development, remain elusive. We developed an antibody-independent method to isolate and map compacted heterochromatin from low cell number samples. We discovered high levels of compacted heterochromatin, H3K9me3-decorated, at protein coding genes in early, uncommitted cells at the germ layer stage, undergoing profound rearrangements and reduction upon differentiation, concomitant with cell type-specific gene expression. Perturbation of the three H3K9me3-related methyltransferases revealed a pivotal role for H3K9me3 heterochromatin during lineage commitment at the onset of organogenesis and for lineage fidelity maintenance.