RNA-seq and H3K27ac ChIP-seq of Y1 cells treated with FGF-2

In addition to driving cell cycle progression, oncogenes may also trigger pathways leading to senescence, thereby inhibiting the growth of tumorigenic cells. Paradoxically, Y1 cells, which carry an amplification of Ras, become senescent after treatment with the mitogen FGF-2. To understand how FGF-2 promotes senescence, we profiled the epigenome, transcriptome, proteome, and phospho-proteome of Y1 cells stimulated with FGF-2. FGF-2 caused delayed acetylation of histone H4 and higher levels of H3K27me3. Sequencing analysis revealed decreased expression of cell cycle-related genes with concomitant loss of H3K27ac. In contrast, FGF-2 promoted the expression of p21 and various cytokines and MAPK-related genes. Nuclear envelope proteins, particularly lamin B1, displayed increased phosphorylation in response to FGF-2. Proteome analysis suggested alterations in cellular metabolism, as evident by modulated expression of enzymes involved in purine biosynthesis, tRNA aminoacylation, and the TCA cycle. Altogether, the response of Y1 cells to FGF-2 is consistent with oncogene-induced senescence. We propose that Y1 cells enter senescence due to deficient cyclin expression and high levels of p21, which may stem from DNA damage or TGFb signaling. Y1 cells were serum-starved for 48 hrs and then treated with FBS alone (10%) or FBS with FGF-2 (10 ng/ml) for 5 hrs. RNA-seq was performed on polyA-enriched RNA in triplicate for each condition. ChIP-seq for H3K27ac was performed on sonicated chromatin extracted from the nuclei of previously frozen cell pellets that were cross-linked with formaldehyde upon thawing. Data was acquired in duplicate for each condition along with input controls.