Figure 1.

Schematic representation of the transcriptome-based design to detect putative direct ETV6 target genes. To identify direct targets of ETV6, we first designed an in vitro RNA-seq experiment using ETV6^−/− Reh-derived clones. Cells were transduced with lentiviral constructs to express ETV6-His and ETV6ΔETS_NLS-His. Total RNA was extracted from stable cell populations and RNA-seq libraries were sequenced. Expression profiles were analyzed using EdgeR. Gene expression profiles in ETV6-His cells were first compared with ETV6ΔETS_NLS-His and pLENTI cells to identify repressed genes (FDR ≤ 0.1). We then included data from the ETV6ΔETS_NLS-His vs. pLENTI comparison and further considered genes whose expression remains constant (P-value≥0.05 or logFC≥−0.5) which are more likely to be direct ETV6 targets. Finally, only genes that showed a specific overexpression in t(12;21)-positive childhood pre-B ALL (pre-B acute lymphoblastic leukemia) patients were considered. ALL: acute lymphoblastic leukemia; FDR; false discovery rate; logCPM: log counts per million reads.