Data from: Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency

Temporal data on gene expression and context-specific open chromatin
states can improve identification of key transcription factors (TFs) and
the gene regulatory networks (GRNs) controlling cellular differentiation.
However, their integration remains challenging. Here, we delineate a
general approach for data-driven and unbiased identification of key TFs
and dynamic GRNs, called EPIC-DREM. We generated time-series
transcriptomic and epigenomic profiles during differentiation of mouse
multipotent bone marrow stromal cell line (ST2) toward adipocytes and
osteoblasts. Using our novel approach we constructed time-resolved GRNs
for both lineages and identifed the shared TFs involved in both
differentiation processes. To take an alternative approach to prioritize
the identified shared regulators, we mapped dynamic super-enhancers in
both lineages and associated them to target genes with correlated
expression profiles. The combination of the two approaches identified aryl
hydrocarbon receptor (AHR) and Glis family zinc finger 1 (GLIS1) as
mesenchymal key TFs controlled by dynamic cell type-specific
super-enhancers that become repressed in both lineages. AHR and GLIS1
control differentiation-induced genes and their overexpression can inhibit
the lineage commitment of the multipotent bone marrow-derived ST2 cells.