Beclin1 Shapes Cardiomyocyte Cell Identity Independent of Its Autophagic Function during Cardiac Reprogramming
This study aimed to compare the transcriptome profiling (RNA-seq) and chromatin accessibility landscape (ATACseq) of induced cardiomyocytes (iCMs) with Beclin1 (Becn1) knockdown and control iCMs (shNT). we generated ATAC-Seq data from day 3 shNT- and shBecn1-treated MGT or control LacZ transduced fibroblasts. We interrogated the enrichment of ATAC-seq reads at +1 and -1 Kb around TSS (Transcription starting site). Comparing MGT-iCMs with LacZ transduced cells, we found that MGT-iCMs gained numerous open chromatin regions compared to LacZ transduced cells. In total, 22,262 high-confidence open chromatin regions were identified when comparing MGT-shNT iCMs with LacZ-shNT cells, and 11,401 open regions were found in MGT-shBecn1 iCMs when comparing to LacZ-shBecn1 cells. However, MGT-shBecn1 iCMs exhibited minimal differences that did not reach statistical significance when compared with MGT-shNT cells. MGT-shBecn1 iCMs had same number of open chromatin regions as the MGT-shNT cells. In parallel, we performed RNA-seq to profile transcriptome changes among day 3 and day 5 shNT- or shBecn1-treated reprogramming and control cells. Next, we profiled the differentially expressed genes (DEGs) at each time point. Gene set enrichment analysis (GSEA) revealed that shBecn1 significantly up-regulated gene sets related to myogenesis, such as those involved in the formation of contractile fiber and myofibril assembly and down-regulated gene sets related to cell proliferation and inflammation. Interestingly, GSEA analysis demonstrated additional enrichment plots of Wnt/ß-Catenin signaling in shBecn1 iCMs. Overall design: mRNA profile and chromatin accessibility profile of neonatal cardiac fibroblasts that were transduced with MGT or control LacZ retroviras plus shBecn1 or shNT treatment.