RNA-Seq of FOXO1 knockdown in Huh-7 cells (single-end Ion Torrent, two biological replicates per condition)
Forkhead Box O-1 (FOXO1) is a regulatory transcription factor involved in apoptosis and cell cycle control and acts as a tumor suppressor. In hepatocellular carcinoma (HCC), FOXO1 is frequently downregulated and associated with poor prognosis. This study investigates FOXO1 as an upstream regulator of long non-coding RNAs in HCC. Public ENCODE ChIP-Seq data and RNA-Seq following FOXO1 knockdown in Huh-7 cells were analyzed. ChIP-Seq analysis identified 982 candidate FOXO1-regulated lncRNAs, while RNA-Seq revealed 131 differentially expressed lncRNAs after knockdown. Integration of both datasets identified 12 lncRNAs with promoter FOXO1 binding and differential expression: ZFAS1, LINC00862, SNHG32, LINC01962, SNHG12, 1QCH-AS1, LINC00324, DCXR-DT, GLUD1P2, FAB5P3, JPX, and SMPD4BP. These represent potential downstream FOXO1 targets in HCC.