A big event always requires a bit of prior preparation, and for evolution, mammalian development is no exception. The mammalian body plans have undergone massive evolutionary rearrangements and diversifications requiring the evolution of complex gene expression profiles. Recent studies in specific tissues in mammalian species have now linked these expression changes to the evolution of regulatory chromatin states (See Cotney et al, Reilly et al, Villar et al, and Prescott et al).
To further investigate the evolution of chromatin states, researchers from the group of David C Page have focused on how bivalent chromatin (H3K4me3 and H3K27me3) in mammalian germ cells influences somatic development. Bivalent chromatin regulates the expression of genes required for lineage-specific somatic differentiation by “poising” them in a repressed state that is ready for quick activation when needed. The team chose germ cells (eggs and sperm) because they carry epigenetic information that influences embryonic development and future somatic gene expression.
The authors tackled bivalent chromatin modifications via ChIP-seq and integrated these findings with RNA-seq to find poised genes in male germ cells from five species (human, rhesus macaque, mouse, bull, and opossum). This helped them to cover around 175 million years of mammalian evolutionary divergence.
So how did this study evolve?
- After considering genes with orthologs in all five species, the study identified 1,200–3,600 genes that contained bivalent domains near their regulatory regions
- Further analysis uncovered 405 bivalent “core poised genes” present in all species analyzed
- Core poised genes are strongly enriched for homeodomain-containing transcription factors
- These factors represent ancient master regulators of gene expression, which mediate embryonic morphology and somatic tissue development.
- Genes that gain bivalent domains in a specific species act downstream of the core genes during development.
- This suggests that the evolution of chromatin states in germ cells parallels the evolution of somatic gene expression and embryo development, and enables the poising of these genes.
- Finally, analysis in chicken germ cells demonstrated that bivalent control of developmental transcriptional regulators in germ cells occurred more than 300 million years ago at the time of the amniote common ancestor of mammals and birds/reptiles
Overall, the study provides evidence that bivalent chromatin domains played an important role early in mammalian evolution and opens the door for future research to discover more about the evolutionary history of bivalent chromatin and also what mechanisms drive chromatin evolution.
Get all the info on this evolving story at Nature Genetics, June 2016.