TOPOCHROMSTEM · Genomic Targets and Function of Topoisomerase II isoforms during Stem Cell Differentiation
FP7 — People (Marie Curie Actions)
- Duration
- 2012-09-01 → 2016-08-31
- EU contribution
- €100,000
- Participants
- 1
- Scheme
- MC-CIG
Lines connect the coordinator with its partners.
Results in brief
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.
Data: CORDIS, © European Union
Project objective
Topoisomerases are enzymes that solve topological problems arising from DNA templated processes such as replication, transcription, recombination and chromatin remodeling. The type II subfamily of Topoisomerases achieve this task by passing a region of duplex from the same or a different molecule through a double-stranded gap generated in DNA. Mammalian cells encode two isoforms of type II enzymes, Topoisomerase II alpha and beta, which have almost identical enzymatic properties in vitro. However, they show very different expression patterns and it is not known whether they differ in their distribution and action sites on the genome and in gene regulatory potential.We find that a switch in the expression from Topo II alpha to beta occurs during neuronal differentiation in vitro and in vivo. We propose to define the chromatin crosstalk of the two Topo II isoforms, alpha and beta, and its contribution to the transcriptome of embryonic stem cells and differentiated neurons respectively. We will combine our sophisticated in vitro mouse differentiation system with genome-wide identification of Topo II alpha binding sites in stem cells. These target sequences will be analyzed for any specific features using computational biology tools and related to the existing datasets of various epigenetic modifications and transcription (Tiwari et al. 2011, Nature Genetics). Using Topo II-specific inhibitors, we will identify Topo II alpha target genes that rely on its catalytic activity for their transcription state. We will next compare the Topo II alpha binding data from stem cells to our recently derived genomewide datasets of Topo II beta binding from neurons. Together, we aim to achieve an understanding of the target preference for the two Topo II isoforms, alpha and beta, with respect to sequence features, genomic regions, chromatin profile and transcription state and their dynamics as proliferating, pluripotent stem cells differentiate into postmitotic neurons.
Original text from CORDIS.
Participants
- INSTITUT FUR MOLEKULARE BIOLOGIE GGMBH · MainzCoordinatorGermany
Links
Data: CORDIS, © European Union