ArticlePloS one2014
High-throughput targeted repeat element bisulfite sequencing (HT-TREBS): genome-wide DNA methylation analysis of IAP LTR retrotransposon.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
- A novel quantitative trait locus implicatesGenome research · 2023Article
- Sperm DNA methylation is predominantly stable in mice offspring born after transplantation of long-term cultured spermatogonial stem cells.Clinical epigenetics · 2023Article
- Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq.Methods in molecular biology (Clifton, N.J.) · 2023Article
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- Review
- Performances of Different Fragment Sizes for Reduced Representation Bisulfite Sequencing in Pigs.Biological procedures online · 2017Article
- Locus-specific hypomethylation of the mouse IAP retrotransposon is associated with transcription factor-binding sites.Mobile DNA · 2017Article
- Integrated small copy number variations and epigenome maps of disorders of sex development.Human genome variation · 2016Article
- DNA methylation variation of human-specific Alu repeats.Epigenetics · 2016Article
- Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing.Genomics data · 2015Article
- Genetic and epigenetic variation among inbred mouse littermates: identification of inter-individual differentially methylated regions.Epigenetics & chromatin · 2015Article
- Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells.Genomics · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
In vertebrates, DNA methylation-mediated repression of retrotransposons is essential for the maintenance of genomic integrity. In the current study, we developed a technique termed HT-TREBS (High-Throughput Targeted Repeat Element Bisulfite Sequencing). This technique is designed to measure the DNA methylation levels of individual loci of any repeat families with next-generation sequencing approaches. To test the feasibility of HT-TREBS, we analyzed the DNA methylation levels of the IAP LTR family using a set of 12 different genomic DNA isolated from the brain, liver and kidney of 4 one-week-old littermates of the mouse strain C57BL/6N. This technique has successfully generated the CpG methylation data of 5,233 loci common in all the samples, representing more than 80% of the individual loci of the five targeted subtypes of the IAP LTR family. According to the results, approximately 5% of the IAP LTR loci have less than 80% CpG methylation levels with no genomic position preference. Further analyses of the IAP LTR loci also revealed the presence of extensive DNA methylation variations between different tissues and individuals. Overall, these data demonstrate the efficiency and robustness of the new technique, HT-TREBS, and also provide new insights regarding the genome-wide DNA methylation patterns of the IAP LTR repeat elements.
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