Genome wide mapping of ETV6 binding sites in pre-B leukemic cells

Benjamin Neveu,Karine Lagacé,Daniel Sinnett,Chantal Richer,Maxime Caron

doi:10.1038/s41598-018-33947-1

Benjamin Neveu, Karine Lagacé + Show 3 more

Open Access

https://doi.org/10.1038/s41598-018-33947-1

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Abstract

Genetic alterations in the transcriptional repressor ETV6 are associated with hematological malignancies. Notably, the t(12;21) translocation leading to an ETV6-AML1 fusion gene is the most common genetic alteration found in childhood acute lymphoblastic leukemia. Moreover, most of these patients also lack ETV6 expression, suggesting a tumor suppressor function. To gain insights on ETV6 DNA-binding specificity and genome wide transcriptional regulation capacities, we performed chromatin immunoprecipitation experiments coupled to deep sequencing in a t(12;21)-positive pre-B leukemic cell line. This strategy led to the identification of ETV6-bound regions that were further associated to gene expression. ETV6 binding is mostly cell type-specific as only few regions are shared with other blood cell subtypes. Peaks localization and motif enrichment analyses revealed that this unique binding profile could be associated with the ETV6-AML1 fusion protein specific to the t(12;21) background. This study underscores the complexity of ETV6 binding and uncovers ETV6 transcriptional network in pre-B leukemia cells bearing the recurrent t(12;21) translocation.

Highlights

Genetic alterations in the transcriptional repressor ETV6 are associated with hematological malignancies
To gain insights into ETV6 function in t(12;21)-positive pre-B leukemia cells, we sought to identify ETV6 binding sites using chromatin immunoprecipitation coupled to high throughput sequencing (ChIP-seq)
Reh cells lack endogenous wild-type ETV6 expression as a result of a t(12;21) translocation and a 12p13 locus deletion. These cells were used for Chromatin immunoprecipitation (ChIP) experiments using the HA epitope as a bait

Summary

Introduction

Genetic alterations in the transcriptional repressor ETV6 are associated with hematological malignancies. The t(12;21) translocation leading to an ETV6-AML1 fusion gene is the most common genetic alteration found in childhood acute lymphoblastic leukemia. To gain insights on ETV6 DNA-binding specificity and genome wide transcriptional regulation capacities, we performed chromatin immunoprecipitation experiments coupled to deep sequencing in a t(12;21)-positive pre-B leukemic cell line. This strategy led to the identification of ETV6-bound regions that were further associated to gene expression. The most common ETV6 aberration is the t(12;21)(p13;q22) translocation which fuses ETV6 to the AML1 gene (or RUNX1) and generates an in-frame ETV6-AML1 chimeric protein[11] This is the most frequent chromosomal abnormality in childhood pre-B cell acute lymphoblastic leukemia (pre-B ALL), occurring in 20% of cases[12]. By including expression data[32], we extensively described ETV6 binding properties and transcriptional activity in this particular context

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