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| Status |
Public on Apr 05, 2021 |
| Title |
DNA methylation analysis by RRBS of UV irradiated human epidermal melanocytes from neonatal foreskin, HEMn-DP2. |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
UVR is the greastest risk factor for melanoma develoment. While the role of UVR in DNA mutagenesis is incontrovertable, is is unclear how UVR induced mutations contribute to melanoma. For example, many of the driver mutations ( BRAF V600E or NRAS Q61R) do not bear the UVR signature C>T mutation. To better understand how UVR is contributing to melanoma development, we investigated the non-mutational effect of UVR on the epigenome, specifically DNA methylation. Aberrant DNA methylation changes are a hallmark in melanoma and there are few reports on the effects of UVR ion DNA methylation. We exposed melanocytes to UVR and cultured them for one-month to detect hertible and stable changes in DNA methylation. We found both hyper and hypo methylated sites after UVR exposure. While many of these changes occured outside of promoters and areas of active gene expression, there were changes in promoter DNA methylation changes that correlated with changes in gene expression. These changes also correlated with those found in melanoma and UVR sensitive sites were prognostic of patient overall survival. Our work shows for the first time UVR induced DNA methylation changes in melanocytes and may be another way in which UVR contributes to melanoma development.
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| Overall design |
Melanocyte cells were UV irradiated with a broad spectrum wave band ( UVA & UVB) for a total dos of 175 J/m2. Cells were cultured for one month before performing reduced representation bisulfite sequencing (RRBS). Genomic DNA was digested by MspI restriction enzyme, which recgonizes the CCGG sequence, and then subjected to bisulfite converstion. Methylated cytosines within CpG's are protected from sodium bisulfite conversion and remain unchanged. Unmethylated cyotosines undergo a reaction with sodium bisulfite resulting in a base change from cytosine to uracil. This base change allows for the detection of methylated versus unmethylated CpG's through high throughput sequencing.
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| Contributor(s) |
Preston-Alp S, Jelinek J, Issa J, Zaidi MR |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Mar 23, 2021 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Sarah Alp |
| E-mail(s) |
tuf08199@temple.edu
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| Organization name |
Temple University
|
| Department |
Fels Institute
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| Lab |
Dr Raza Zaidi
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| Street address |
3307 N Broad Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19140 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA716678 |
| SRA |
SRP311864 |
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