Gcn5 regulates FGF signaling outputs through c-Myc during early differentiation of embryoid bodies [RNA-Seq]

Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers. How particular chromatin modifying enzymes affect specific developmental processes is not well defined. Here we report that Gcn5, a HAT essential for embryonic development, is largely required for c-MYC target gene transcription downstream of FGF signaling in early embryoid bodies (EBs). Gcn5 null EBs display deficient activation of ERK and p38, disorganized cytoskeletal networks, and compromised capacity to differentiate toward mesodermal and endodermal lineages. These findings establish a regulatory role for Gcn5 in execution of a critical signaling pathway during early development. To determine changes in gene expression profile upon Gcn5 loss at early differentiation stages, RNA from day 3 and day 5 EBs differentiated from Gcn5 fx/fx (4_1) and Gcn5-/-(4_C2) ES cells were isolated for deep sequencing, in duplicates. Key genes identified from RNAseq were validated by qRT-PCR using a second biological pair of Gcn5fxf/x and Gcn5-/- cells.