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Updated: Jun 2, 2026
Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
Published on: June 27, 2020
Oncogenic fusion protein EWS/FLI1 down-regulates gene expression by both transcriptional and posttranscriptional
Kelly A France1, Jennifer L Anderson, Ann Park
1Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.
Abstract:
Ewing family tumors are characterized by a translocation between the RNA binding protein EWS and one of five ETS transcription factors, most commonly FLI1. The fusion protein produced by the translocation has been thought to act as an aberrant transcription factor, leading to changes in gene expression and cellular transformation. In this study, we investigated the specific processes EWS/FLI1 utilizes to alter gene expression. Using both heterologous NIH 3T3 and human Ewing Family Tumor cell lines, we have demonstrated by quantitative pre-mRNA analysis that EWS/FLI1 repressed the expression of previously validated direct target genes at the level of transcript synthesis. ChIP experiments showed that EWS/FLI1 decreases the amount of Pol II at the promoter of down-regulated genes in both murine and human model systems. However, in down-regulated target genes, there was a significant disparity between the modulation of cognate mRNA and pre-mRNAs, suggesting that these genes could also be regulated at a posttranscriptional level. Confirming this, we found that EWS/FLI1 decreased the transcript half-life of insulin-like growth factor binding protein 3, a down-regulated direct target gene in human tumor-derived Ewing's sarcoma cell lines. Additionally, we have shown through reexpression experiments that full EWS/FLI1-mediated transcriptional repression requires intact EWS and ETS domains. Together these data demonstrate that EWS/FLI1 can dictate steady-state target gene expression by modulating both transcript synthesis and degradation.
Insights
Ewing family tumors involve EWS/FLI1 fusion proteins altering gene expression. This study reveals EWS/FLI1 impacts both gene transcription and RNA degradation, offering new insights into tumor development.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Ewing family tumors (EFTs) are driven by specific chromosomal translocations.
- The EWS/FLI1 fusion protein is a hallmark of EFTs, implicated in cellular transformation.
- The precise mechanisms by which EWS/FLI1 alters gene expression remain incompletely understood.
Purpose of the Study:
- To elucidate the molecular mechanisms through which the EWS/FLI1 fusion protein regulates target gene expression.
- To investigate whether EWS/FLI1 affects gene expression at transcriptional and/or post-transcriptional levels.
Main Methods:
- Quantitative pre-mRNA analysis in NIH 3T3 and human EFT cell lines.
- Chromatin immunoprecipitation (ChIP) to assess Polymerase II (Pol II) occupancy.
- Transcript half-life measurements for specific target genes.
- Reexpression experiments to validate the role of EWS and ETS domains.
Main Results:
- EWS/FLI1 represses the expression of direct target genes at the level of transcript synthesis.
- EWS/FLI1 reduces Pol II recruitment to the promoters of down-regulated genes.
- EWS/FLI1 decreases the transcript half-life of specific target genes, such as insulin-like growth factor binding protein 3.
- Intact EWS and ETS domains are required for full transcriptional repression by EWS/FLI1.
Conclusions:
- EWS/FLI1 modulates steady-state target gene expression through a dual mechanism.
- This involves the regulation of both transcript synthesis and transcript degradation.
- These findings provide a comprehensive understanding of EWS/FLI1's role in EFT pathogenesis.
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