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. Author manuscript; available in PMC: 2018 Jul 10.
Published in final edited form as: Cancer Cell. 2017 Jul 10;32(1):101–114.e8. doi: 10.1016/j.ccell.2017.06.002

Figure 5.

Figure 5

NELFE preferentially interacts with MYC-related genes. (A) 7-mer Z scores and motifs for the two probe sets for NELFE (left). Differentially (DEGs) and undifferentially (uDEGs) expressed genes were scanned for NELFE motifs (right) (***p=3.7×10−49). (B) ChIP-Seq ENCODE analysis of 1,836 DEGs that were predicted as NELFE associated genes from (A). Showing only the MYC and its family members. (C) RNA immunoprecipitation followed by RT-PCR analysis of MYC-related and NELFE associated genes (CCL20, PA2G4, CCNE2, IER2 and SERPINE1) and MYC-related genes that is not an NELFE predicted gene (SYNGR2). (D) Venn diagram of 1,445 genes whose NELFE RNA consensus sequence was found in the 3′UTR, 5′UTR or CDS. (E) RT-PCR of Huh1 cells after 72 hr of specified siRNA (top) or 16 hr of 10058-F4 treatment (bottom). (F) RT-PCR of MYC-related genes in Huh1 cells after NELFE siRNA followed by Actinomycin D treatment (10 μg/ml) over time. Dotted lines are at 50% mRNA remaining. (G) Synthetic RNA oligos with the indicated NELFE consensus sequences for PA2G4 or CCNE2 (Top) were examined via RNA pull down and blotted for NELFE (Bottom: cropped immunoblot). All data are mean ± SD. See also Figure S5 and Table S4.