ChIP-seq analysis on C11orf95-RELA fusion expressing cells

Ependymomas are the primary glial tumors that can occur in all ages and locations of the central nervous system. Recurrent C11orf95-RELA fusion (RELAFUS) genes were identified in a large fraction of the supratentorial ependymomas. RELAFUS1 (Type 1) and RELAFUS2 (Type 2), the two most frequent fusion variants were potent driver oncogenes capable of inducing human ependymoma-like tumors in mice, thus likely being responsible for the tumor formation in human patients. Here, we explored transcriptional target genes directly regulated by RELAFUS protein using HA-tag ChIP-seq analyses in the RELAFUS expressing cells and dissected the oncogenic program underlying the ependymoma formation. Overall design: (1) HA-tag ChIP-seq on the 293T/tv-a cells retrovirally infecting the RCAS-RELAFUS1-HA and RELAFUS1-S486E-HA (S486E, RELAFUS1 mutant which was severely impaired the tumor-forming capacity) each with two replicates. (2) HA-tag ChIP-seq on mouse ependymoma (mEPN) cells derived from the RCAS-RELAFUS1-HA tag-driven ependymoma (H1203 cells) with two replicates. (3) H3K27ac ChIP-seq on two mouse ependymoma-derived cell lines (H41 and H1203 cells) each with two replicates.