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| Status |
Public on Feb 14, 2019 |
| Title |
Genome-wide map of proximity linkage to renin proximal promoter in rat |
| Organism |
Rattus norvegicus |
| Experiment type |
Other
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| Summary |
Physical proximity mapping through sequencing can provide an unbiased view of the chromatin close to the proximal promoter of the renin gene (Ren). Our objective was to determine genomic regions that physically interact with the renin proximal promoter, using two different genetic backgrounds, the Dahl salt sensitive and normotensive SS-13BN, which have been shown to have different regulation of plasma renin in vivo. The chromatin conformation capture method with sequencing focused at the Ren proximal promoter in rat-derived cardiac endothelial cells was used. Cells were fixed, chromatin close to the Ren promoter was captured, and fragments were sequenced. The clustering of mapped reads produced a genome-wide map of chromatin in contact with the Ren promoter. The largest number of contacts was found on chromosome 13, the chromosome with Ren, and contacts were found on all other chromosomes except chromosome X. These contacts were significantly enriched with genes positively correlated with Ren expression and with mapped quantitative trait loci (QTLs) associated with blood pressure, cardiovascular and renal phenotypes. The results were reproducible in an independent biological replicate and in endothelial cells derived from a second rat stain. The findings reported here represent the first map between a critical cardiovascular gene and physical interacting loci throughout the genome, and will provide the basis for several new directions of research.
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| Overall design |
4C-seq contact maps at Renin proximal promoter viewpoint in Rat cardiac endothelial cells from SS and SS13BN strains
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| Web link |
http://10.1152/physiolgenomics.00132.2017
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| Contributor(s) |
Stodola TJ, Liu P, Liu Y, Vallejos AK, Geurts AM, Greene AS, Liang M |
| Citation(s) |
29521603 |
| Submission date |
Feb 15, 2018 |
| Last update date |
May 16, 2019 |
| Contact name |
Mingyu Liang |
| E-mail(s) |
mliang@mcw.edu
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| Organization name |
Medical College of Wisconsin
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| Department |
Physiology
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| Street address |
8701 Watertown Plank Rd
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| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53226 |
| Country |
USA |
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| Platforms (1) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA434196 |
| SRA |
SRP132913 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110652_RAW.tar |
67.4 Mb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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