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| Status |
Public on Oct 27, 2016 |
| Title |
DNA methylation variation of human-specific Alu repeats |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
DNA methylation is the major repression mechanism for human retrotransposons, such as the Alu family. Here, we have derived methylation levels regarding 5238 loci belonging to two Alu subfamilies, AluYa5 and AluYb8, using High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS). The results indicate that ~90% of loci are repressed by high methylation levels. Of the remaining loci, many of these hypomethylated elements are found near gene promoters and show high levels of DNA methylation variation. We have characterized this variation in the context of tumorigenesis and inter-individual differences. Comparison of a primary breast tumor and its matched normal tissue revealed early DNA methylation changes in ~1% of AluYb8 elements in response to tumorigenesis. At the same time, AluYa5/Yb8 elements proximal to promoters also showed differences in methylation of up to one order of magnitude even between normal individuals. Overall, the current study demonstrates that early loss of methylation occurs during tumorigenesis in a subset of young Alu elements, suggesting their potential clinical relevance. However, techniques such as deep-bisulfite-sequencing of individual loci using HT-TREBS are required to distinguish clinically relevant loci from the background observed for AluYa5/Yb8 elements in general with regard to high levels of inter-individual variation in DNA methylation.
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| Overall design |
HT-TREBS has been used with the Ion Torrent PGM platform to analyze the DNA methylation of 5238 AluYa5/Yb8 elements in a locus-specific manner in human skin-derived fibroblast cells, and a matched normal breast and primary tumor
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| Contributor(s) |
Bakshi A, Herke S, Batzer M, Kim J |
| Citation(s) |
26890526 |
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| Submission date |
Oct 28, 2015 |
| Last update date |
Oct 04, 2019 |
| Contact name |
Joomyeong Kim |
| E-mail(s) |
jkim@lsu.edu
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| Organization name |
Louisiana State University
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| Department |
Biological Sciences
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| Street address |
202 Life Sciences Bldg
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| City |
Baton Rouge |
| State/province |
LA |
| ZIP/Postal code |
70803 |
| Country |
USA |
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| Platforms (1) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA300357 |
| SRA |
SRP065386 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE74420_RAW.tar |
160.0 Kb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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