S6K1 is a key regulator of cell growth/size and metabolism. In contrast to the established role of cytosolic S6K1 in these cellular processes, the function of S6K1 in the nucleus remains poorly understood. Our recent study revealed that S6K1 is translocated into the nucleus upon adipogenic stimulus, directly binding to and phosphorylating H2B at serine 36. This phosphorylation promotes EZH2 recruitment and subsequent histone H3K27 trimethylation on the promoter of its target genes including Wnt6, Wnt10a, and Wnt10b, leading to the repression of their expression. The S6K1-mediated suppression of the Wnt genes facilitates adipogenic differentiation through the expression of adipogenic transcription factors, PPARγ and Cebpa. Consistently, white adipose tissues from S6K1-deficient mice exhibit the marked reduction in H2BS36 phosphorylation (H2BS36p) and H3K27 trimethylation (H3K27me3), leading to the enhanced expression of the Wnt genes. In addition, levels of H2BS36p and H3K27me3 are highly elevated in white adipose tissues from mice fed on a high-fat diet or from obese humans. These findings describe a novel role of S6K1 as a transcriptional regulator controlling an epigenetic network initiated by phosphorylation of H2B and trimethylation of H3, acting to shut off Wnt gene expression in early adipogenesis.