Transcription factor 21 regulates cardiac myofibroblast formation and fibrosis [ChIP-Seq]
Transcription factor 21 (TCF21) is a basic helix-loop-helix protein required for developmental specification of cardiac fibroblasts from epicardial progenitor cells that normally surround and invade the heart. In the adult heart, TCF21 is expressed in tissue resident fibroblasts but is downregulated in response to injury or stimuli leading to myofibroblast differentiation. These findings led to the hypothesis that Tcf21 could be a regulator of fibroblast cell-fate in the adult mammalian heart and contribute to cardiac fibrosis. Here, chromatin immunoprecipitation followed by sequencing was used to identify TCF21 genome occupancy in adult cardiac fibroblasts. Overall design: Col1a1-TCF21 mice were generated that express TCF21 upon Cre mediated recombination. TCF21 genome-wide occupancy was evaluated by chromatin immunoprecipitation and sequencing (ChIP-seq) in isolated cardiac fibroblasts isolated from Col1a1-TCF21 hearts. Fibroblasts were infected with an adenovirus encoding Cre recombinase to induce expression of TCF21 and expanded for 5 days. Transforming growth factor b1 was added in the last 24 hours to further promote fibroblast activation and ChIP-seq was performed. ChIP-seq data were analyzed with the Trim Galore Chip-seq paired-end reads pipeline (https://github.com/datirium/workflows/blob/master/workflows/trim-chipseq-pe.cwl) in the Scientific Data Analysis Platform, SciDAP (https://scidap.com/) (Datirium). Adapters were trimmed using Trim Galore (https://github.com/FelixKrueger/TrimGalore) and the reads were aligned to the mouse genome assembly mm10/GRCm38 using Bowtie17. Peak-calling was performed with MACS218.  The UCSC Genome Browser's bedGraphToBigWig tool was used to produce a bigWig file. Genome browser tracks were created with the genome coverage in BEDTools19 and normalized to total mapped read number and displayed as coverage on IGV browser20.