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A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution.

Xavier Grau-BovéCristina NavarreteCristina ChivaThomas PribasnigMeritxell AntóGuifré TorruellaLuis Javier GalindoBernd Franz LangDavid MoreiraPurificacion Lopez-GarciaIñaki Ruiz-TrilloChrista SchleperEduard SabidóArnau Sebé-Pedrós
Published in: Nature ecology & evolution (2022)
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (for example, methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.
Keyphrases
  • transcription factor
  • genome wide
  • dna damage
  • gene expression
  • dna methylation
  • single cell
  • magnetic resonance imaging
  • oxidative stress
  • mesenchymal stem cells
  • genetic diversity