Pingzhu Zhou, Nathan J. VanDusen, Yanchun Zhang, Yangpo Cao, Isha Sethi et al.
Cardiomyocyte differentiation continues throughout murine gestation and into the postnatal period, driven by temporally regulated expression changes in the transcriptome. The mechanisms that regulate these developmental changes remain incompletely defined. Here we used cardiomyocyte specific ChIP-seq of the activate enhancer marker P300 to identify 54,920 cardiomyocyte enhancers at seven stages of murine heart development. These data were matched to cardiomyocyte gene expression profiles at the same stages and Hi-C and H3K27ac HiChIP chromatin conformation data at fetal, neonatal, and adult stages. Regions with dynamic P300 occupancy exhibited developmentally regulated enhancer activity, as measured by massively parallel reporter assays in cardiomyocytes in vivo, and identified key transcription factor binding motifs. These dynamic enhancers interacted with temporal changes of 3D genome architecture to specify developmentally regulated cardiomyocyte gene expression. Our work provides a 3D genome-mediated enhancer activity landscape of murine cardiomyocyte development.
Pingzhu Zhou, Nathan J. VanDusen, Yanchun Zhang, Yangpo Cao, Isha Sethi, Rong Hu, Shuo Zhang, Guangyu Wang, Lincai Ye, Neil Mazumdar, Jian Chen, Xiaoran Zhang, Yuxuan Guo, Bin Li, Qing Ma, Julianna Y. Lee, Weiliang Gu, Guo-Cheng Yuan, Bing Ren, Kaifu Chen, William T. Pu. Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation. 2023-05-22. https://doi.org/10.1016/j.devcel.2023.03.020
An in vivo AAV9 MPRA tested 190-bp wild-type and motif-shuffled mutant pairs centered on candidate nuclear-receptor motifs in Early and Late P300 regions, along with positive and negative controls. The library was delivered subcutaneously to P0 pups and ventricular reporter RNA was measured at P7 across 14 biological replicates.
An in vivo AAV9 MPRA tested 400-bp mouse genomic regions centered on dynamic Early and Late P300 regions, together with static, positive-control, and negative-control elements. The library was delivered to E15.5 embryos for P0 collection or to P0 pups for P7 and P28 collection, and enhancer activity was measured from ventricular mCherry RNA relative to AAV DNA.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 6 files (ZIP)Data_S2_MPRA_dynamic_P300_regions.xlsxData_S3_NR_motif_ablation.xlsxGSE196346_NR-MPRA_counts.csv.gzGSE196346_P300-MPRA_counts.csv.gzREADME.txtSupplementary_Table_S1_and_figures.pdf