GSE124008
A reference map of cardiac transcription factor chromatin occupancy identifies dynamic and conserved transcriptional enhancers
Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering the transcriptional programs that orchestrate organ development and homeostasis. Here we used biotinylated knockin alleles of seven key TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) that regulate heart development and homeostasis to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult heart. Our results show that these TFs have dynamic chromatin occupancy between developmental stages. We observed that multiple TFs often co-occupy the same chromatin region, exhibiting collaborative binding that overall was most consistent with indirect cooperativity. Regions with multiple TF binding were more likely to exhibit features of functional regulatory elements, including evolutionary conservation, chromatin accessibility, and activity in transcriptional enhancer assays. Although histone H3 acetylation on lysine 27 (H3K27ac) has been used to identify active enhancers, many regions occupied by multiple TFs lacked H3K27ac, and TF-bound regions with or without H3K27ac co-occupancy had similar region conservation and enhancer activity. Specific studies of TEAD1 demonstrated that it is a core component of the cardiac transcriptional network: physically interacted with NKX2-5 and MEF2C and co-occupied regulatory loci with other cardiac TFs to regulate cardiomyocyte-specific gene functions. Our study shows that co-occupancy by multiple TFs is a hallmark of a subset of functional transcriptional regulatory elements and provides a rich resource for deciphering the cardiac transcriptional regulatory network. Overall design: Examination of cardiac TF binding in fetal (E12.5) and adult mouse heart ventricles using BioChIP-Seq. Examination of cardiac TF binding in fetal (E12.5) and adult mouse heart ventricles.