Ancient and animal-specific regulatory modes of EWS::FLI1 revealed by a minimal yeast model.
4 affiliations
- 1Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.
- 2Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona 08950, Spain.
- 3Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona 08950, Spain.
- 4Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
Abstract
Ewing sarcoma (EwS) is an aggressive, human-exclusive tumor typically driven by the EWS::friend leukemia integration 1 (FLI1) fusion protein. To assess whether EWS::FLI1's neomorphic functions depend on evolutionarily recent cofactors, we expressed EWS::FLI1 in Saccharomyces cerevisiae, a minimal system in which the BAF complex is strongly diverged and ETS transcription factors (ETS-TFs), polycomb group (PcG) proteins, and CBP/p300 are absent. We used co-IP/mass spectrometry to map the yeast interactome, ChIP-seq to identify gDNA binding sequences, RNA-seq for gene expression, and engineered reporters to test conversion of GGAA tandem repeats (GGAAμSat) into neoenhancers. We found that the yeast EWS::FLI1 interactome was limited and distinct from its human counterpart, sharing core machinery (RNA polymerase II, FACT) but lacking BAF/SWI-SNF and spliceosome complexes, and showing enrichment for SAGA. EWS::FLI1 binds to hundreds of yeast genomic sites with preference for putative ETS-TF consensus sequences and CA dinucleotide repeats, and redirects RNA polymerase II to EWS::FLI1-bound loci. Yet, EWS::FLI1-expressing cells presented only minimal transcriptional dysregulation, in contrast to the extensive changes observed in human and Drosophila cells. Finally, EWS::FLI1 successfully converted silent GGAAμSat sequences into active enhancers in yeast. This remarkable result occurs despite the absence of homologs for key human activators, such as CBP/p300, suggesting that EWS::FLI1 can mobilize functionally related, nonhomologous pathways to establish neoenhancers at GGAAμSat sites. Altogether, our results indicate that EWS::FLI1's core ability to drive GGAAμSat-dependent gene expression is a conserved, ancient property, while GGAAμSat-independent extensive transcriptome reprogramming depends on animal-specific cofactors and pathways.
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BibTeX
@article{velazquez2026ancient,
title = {{Ancient and animal-specific regulatory modes of EWS::FLI1 revealed by a minimal yeast model.}},
author = {Diego Velázquez and Cristina Molnar and Jose Reina and Jaume Mora and Cayetano Gonzalez},
journal = {PNAS nexus},
year = {2026},
month = sep,
doi = {10.1093/pnasnexus/pgag329},
url = {https://europepmc.org/article/MED/42857501},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Ancient and animal-specific regulatory modes of EWS::FLI1 revealed by a minimal yeast model.
AU - Diego Velázquez
AU - Cristina Molnar
AU - Jose Reina
AU - Jaume Mora
AU - Cayetano Gonzalez
PY - 2026
DA - 2026/09/28
JO - PNAS nexus
DO - 10.1093/pnasnexus/pgag329
UR - https://europepmc.org/article/MED/42857501
AB - Ewing sarcoma (EwS) is an aggressive, human-exclusive tumor typically driven by the EWS::friend leukemia integration 1 (FLI1) fusion protein. To assess whether EWS::FLI1's neomorphic functions depend on evolutionarily recent cofactors, we expressed EWS::FLI1 in Saccharomyces cerevisiae, a minimal system in which the BAF complex is strongly diverged and ETS transcription factors (ETS-TFs), polycomb group (PcG) proteins, and CBP/p300 are absent. We used co-IP/mass spectrometry to map the yeast interactome, ChIP-seq to identify gDNA binding sequences, RNA-seq for gene expression, and engineered reporters to test conversion of GGAA tandem repeats (GGAAμSat) into neoenhancers. We found that the yeast EWS::FLI1 interactome was limited and distinct from its human counterpart, sharing core machinery (RNA polymerase II, FACT) but lacking BAF/SWI-SNF and spliceosome complexes, and showing enrichment for SAGA. EWS::FLI1 binds to hundreds of yeast genomic sites with preference for putative ETS-TF consensus sequences and CA dinucleotide repeats, and redirects RNA polymerase II to EWS::FLI1-bound loci. Yet, EWS::FLI1-expressing cells presented only minimal transcriptional dysregulation, in contrast to the extensive changes observed in human and Drosophila cells. Finally, EWS::FLI1 successfully converted silent GGAAμSat sequences into active enhancers in yeast. This remarkable result occurs despite the absence of homologs for key human activators, such as CBP/p300, suggesting that EWS::FLI1 can mobilize functionally related, nonhomologous pathways to establish neoenhancers at GGAAμSat sites. Altogether, our results indicate that EWS::FLI1's core ability to drive GGAAμSat-dependent gene expression is a conserved, ancient property, while GGAAμSat-independent extensive transcriptome reprogramming depends on animal-specific cofactors and pathways.
SN - 2752-6542
ER -