EpiTEome: Simultaneous Detection of Transposable Element Insertion Sites and their DNA Methylation Levels
TS-036524 — A new software program that detects both transposable element insertion sites and their methylation states from a single DNA methylation sequencing dataset.
Transposable elements are fragments of DNA within plant, animal and fungal genomes that have the distinct capabilities to duplicate and insert into the genome, causing mutations and alterations in gene regulation. Tracking when transposable elements move and where they insert requires high-cost wh…
Transposable elements are fragments of DNA within plant, animal and fungal genomes that have the distinct capabilities to duplicate and insert into the genome, causing mutations and alterations in gene regulation. Tracking when transposable elements move and where they insert requires high-cost whole genome resequencing. Transposable elements are also the targets of the epigenetic modification of DNA methylation, which cells use to mark and inhibit transposable element regions of their genomes. Genome-wide datasets to detect DNA methylation (MethylC-seq) only assay the reference genome and thus reference transposable element positions, presenting a gap in detection capability of the DNA methylation of new or non-reference position transposable element insertion sites. Assaying the DNA methylation level of new or non-reference position transposable element insertion sites currently requires two costly datasets: genome resequencing (to identify the insertion sites) and MethylC-seq (to assay DNA methylation levels).
- As of 2015, the global epigenetics market was valued at $470 million, with the market projected to increase to $890 million by 2020, realizing a CAGR of 13.6% over the five year period. This double digit growth will be largely attributable to numerous factors, including the increasing rate of cancer diagnoses globally, the growing volume of R&D spend from biotechnology firms, and an increase in epigenetic applications for non-oncology diseases.
- Epigenetics research and development is largely focused in North America and Western Europe, with companies such as Merick & Co., Thermo Fisher Scientific inc., QIAGEN N.V., SigmaAldrich Corporation and Illumina inc. capturing the majority of market share.
Researchers at the Ohio State University's Department of Molecular Genetics, have developed a software application to detect both new transposable element insertion site positions and their methylation states from a single MethIC-seq dataset. Named EpiTEome, the software initiates analysis with MethylC-seq reads generated from whole genome sequencing of bisulfite-converted DNA. As a result of this development focus, EpiTEome outperforms other split read transposable element insertion site detection programs, even while functioning on bisulfite-converted reads. Additionally, the program characterizes the previously discarded fraction of DNA methylation at positions of new transposable element insertions, enabling investigations into the epigenetic regulation of non-reference or transposed transposable elements.