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| Status |
Public on Jan 28, 2022 |
| Title |
Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration |
| Organism |
Danio rerio |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The epicardium is a mesothelial tissue layer that envelops the heart. Cardiac injury activates dynamic gene expression programs in epicardial tissue, which in the case of zebrafish enables subsequent regeneration through paracrine and vascularizing effects. To identify tissue regeneration enhancer elements (TREEs) that control injury-induced epicardial gene expression during heart regeneration, we profiled transcriptomes and chromatin accessibility in epicardial cells purified from regenerating zebrafish hearts. We identified hundreds of candidate TREEs, defined by increased chromatin accessibility of non-coding elements near genes with increased expression during regeneration. Several of these candidate TREEs were incorporated into stable transgenic lines, with 5 of 6 elements directing injury-induced epicardial expression but not ontogenetic expression in hearts of larval animals. Whereas two independent TREEs linked to the gene gnai3 showed similar functional features of gene regulation in transgenic lines, two independent ncam1a-linked TREEs directed distinct spatiotemporal domains of epicardial gene expression. Thus, multiple TREEs linked to a regeneration gene can possess either matching or complementary regulatory controls. Our study provides a new resource and principles for understanding the regulation of epicardial genetic programs during heart regeneration.
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| Overall design |
ATAC-sequencing and RNA-sequencing of isolated epicardial cells from uninjured zebrafish hearts and hearts after amputation injury
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| Contributor(s) |
Cao Y, Ou J, Song L, Safi A, Crawford GE, Poss KD, Cao J |
| Citation(s) |
35179181 |
| Submission date |
Nov 02, 2016 |
| Last update date |
Feb 19, 2022 |
| Contact name |
Jingli Cao |
| E-mail(s) |
jic4001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Cell & Developmental Biology
|
| Lab |
Jingli Cao
|
| Street address |
413 E 69th ST, BRB-518
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
| GPL21741 |
Illumina HiSeq 4000 (Danio rerio) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA352230 |
| SRA |
SRP092500 |
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