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Identifying co‐opted transposable elements using comparative epigenomics
Author(s) -
Venuto David,
Bourque Guillaume
Publication year - 2018
Publication title -
development, growth and differentiation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.864
H-Index - 66
eISSN - 1440-169X
pISSN - 0012-1592
DOI - 10.1111/dgd.12423
Subject(s) - transposable element , epigenomics , computational biology , biology , computer science , evolutionary biology , genetics , genome , dna methylation , gene , gene expression
The human genome gives rise to different epigenomic landscapes that define each cell type and can be deregulated in disease. Recent efforts by ENCODE , the NIH Roadmap and the International Human Epigenome Consortium ( IHEC ) have made significant advances towards assembling reference epigenomic maps of various tissues. Notably, these projects have found that approximately 80% of human DNA was biochemically active in at least one epigenomic assay while only approximately 10% of the sequence displayed signs of purifying selection. Given that transposable elements ( TE s) make up at least 50% of the human genome and can be actively transcribed or act as regulatory elements either for their own purposes or be co‐opted for the benefit of their host; we are interested in exploring their overall contribution to the “functional” genome. Traditional methods used to identify functional DNA have relied on comparative genomics, conservation analysis and low throughput validation assays. To discover co‐opted TE s, and distinguish them from noisy genomic elements, we argue that comparative epigenomic methods will also be important.