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| Status |
Public on Sep 20, 2020 |
| Title |
Beclin1 Shapes Cardiomyocyte Cell Identity Independent of Its Autophagic Function during Cardiac Reprogramming |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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/β-Catenin signaling in shBecn1 iCMs.
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| 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.
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| Contributor(s) |
Wang L, Ma H, Yang Y, Qian L |
| Citation(s) |
33087505 |
| Submission date |
Jun 30, 2020 |
| Last update date |
Dec 22, 2020 |
| Contact name |
Li Wang |
| E-mail(s) |
wali@email.unc.edu
|
| Phone |
9199374137
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
UNC
|
| Lab |
Li Qian
|
| Street address |
111 Mason Farm Rd, Chapel Hill, NC 27599
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27514 |
| Country |
USA |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA643238 |
| SRA |
SRP269388 |
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