Updated project metadata. Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have design an experimental strategy to survey the chromatome of proliferating cells by using the DNA-mediated chromatin pull-down technology (Dm-ChP). Our approach provides a global view of cellular chromatome in normal physiological conditions and enables the identification of chromatin-bound proteins de novo. Integrating Dm-ChP with genomic and functional data, we have discovered an unexpected chromatin function for adenosylhomocysteinase (AHCY), a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production, and cell division during early phase of embryo development, in which the metabolic flux of methylation reactions is favored in a local milieu