Final Report Summary - TOPOCHROMSTEM (Genomic Targets and Function of Topoisomerase II isoforms during Stem Cell Differentiation)
DNA topoisomerases are among the most conserved proteins. They have a key function in relieving torsional stress of DNA during fundamental cellular processes such as replication, transcription, recombination, chromatin remodelling, chromosome condensation and segregation. Mammals have two classes of topoisomerases: Type I, that pass one strand of DNA through a break in the opposing strand and type II, that pass a region of duplex from the same or a different molecule through a double-stranded gap generated in the DNA. However, their function in gene regulation, especially during cellular differentiation, remained unknown. Here we find that the expression of topo II isoforms, topoisomerase IIα and topoisomerase IIβ, is the characteristic of dividing and postmitotic tissues, respectively. In embryonic stem cells, topoisomerase IIα preferentially occupies active gene promoters. Topoisomerase IIα inhibition compromises genomic integrity, which results in epigenetic changes, altered kinetics of RNA Pol II at target promoters and misregulated gene expression. Common targets of topoisomerase IIα and topoisomerase IIβ are housekeeping genes, while unique targets are involved in proliferation/pluripotency and neurogenesis, respectively (Fig 1). Topoisomerase IIα targets exhibiting bivalent chromatin resolve upon differentiation, concomitant with their activation and occupancy by topoisomerase IIβ, features further observed for long genes. These long silent genes display accessible chromatin in embryonic stem cells that relies on topoisomerase IIα activity. These findings suggest that topoisomerase IIα not only contributes to stem-cell transcriptome regulation but also primes developmental genes for subsequent activation upon differentiation. Our findings provoke for a major paradigm shift in the concepts of how labour is divided between the two topo II isoforms and how these enzymes are involved in gene regulation. It is very exciting to uncover how these enzymes, classically known to support chromosomal integrity by resolving torsional stress, participate in gene regulatory networks that is not only important for maintenance of cell-identity but also for developmental decisions. Future work should aim to unravel how the collaborative partnership between the two topo II isoforms contributes to transcriptional reprogramming underlying tri-lineage differentiation during embryonic development.