An in vivo repertoire of zebrafish cardiomyocyte-specific cis-regulatory elements [ChIP-Seq]

cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocytes-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share a number of physiological features with the human heart during development. Therefore, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Cardiomyocytes were isolated from the Tg(myl7::GFP) zebrafish transgenic line. Larvae were collected 72 hpf (hours post fertilization). GFP-positive (30,000 cells, n=3 biological replicates) and GFP-negative cells (30,000 cells, n=3 biological replicates) were collected, and ChIP-sequencing was performed on these samples. The raw ChIP-seq FASTQ files are provided in SRA. The supplementary files are: the BED file containing differential peaks only found in GFP-negative samples (GSM7995224_GFP-_only.bed.gz), the BED file containing differential peaks only found in GFP-positive samples (GSM7995227_GFP+_only.bed.gz).