Epigenetic control of metabolic identity across cell types.

Background: Constraint-based network modeling is a powerful genomic-scale approach for analyzing cellular metabolism, capturing metabolic variations across tissues and cell types, and defining the metabolic identity essential for identifying disease-associated transcriptional states. Results: Using RNA-seq and epigenomic data from the EpiATLAS resource of the International Human Epigenome Consortium (IHEC), we reconstructed metabolic networks for 1,555 samples spanning 58 tissues and cell types. Analysis of these networks revealed the distribution of metabolic functionalities across human cell types and provides a compendium of human metabolic activity. This integrative approach allowed us to define, across tissues and cell types, i) reactions that fulfil the basic metabolic processes (core metabolism), and ii) cell type-specific functions (unique metabolism), that shape the metabolic identity of a cell or a tissue. Integration with EpiATLAS-derived cell-type-specific gene-level chromatin states and enhancer-gene interactions identified enhancers, transcription factors, and key nodes controlling core and unique metabolism. Transport and first reactions of pathways were enriched for high expression, active chromatin state, and Polycomb-mediated repression in cell types where pathways are inactive, suggesting that key nodes are targets of repression. Discussion: This integrative analysis forms the basis for identifying regulation points that control metabolic identity in human cells.