Whole-genome IAP methylation data for mouse sperm and tail DNA.. Mus musculus

IAP is one of the most transpositinally active retrotransposons in the mouse. Its transcription starts from the 5' long terminal repeat (LTR), and the expression level varied between cell types. This variation is thought to arise from differences in the epigenetic states, such as DNA methylation, of some copies of the 5' LTR between the cells. However, due to the high copy number and high sequence similarity, it was difficult to comprehensively and individually analyze epigenetic state of the IAP LTRs. Here, we developed a method called TEPBAT (Target Enrichment after Post-Bisulfite Adaptor Tagging) to analyze DNA methylation of individual retrotransposon copies. Using the method, we determined DNA methylation levels of >8,500 copies of genomic IAP LTRs (>97% of the copies targeted by the PCR primer) in sperm and tail. This revealed that the vast majority of the LTRs were heavily methylated both in sperm and tail, but hypomethylated copies were more frequently found in sperm than in tail. Interestingly, most of these hypomethylated LTRs were solo-type, belonged to specific subfamilies, and carried binding sites for transcription factors (TFs) active in male germ cells. We discuss possible roles for these TF-binding sites and the IAP internal sequence in regulation of LTR methylation. Overall design: To study DNA methylation levels of individual IAP LTR loci comprehensively, genomic DNA was treated with bisulfite and the complementary strands were synthesized by PBAT. IAP LTR loci were then selectively amplified by PCR. The PCR products were ligated to the Illumina adaptor, followed by HiSeq sequencing (a lane per sample).