Abstract
Transposable elements (TEs) have deposited functional regulatory elements throughout the human genome. Although most are silenced, certain TEs have been co-opted by the host. However, a comprehensive, multidimensional picture of the contribution of TEs to normal human gene regulation is still lacking. Here, we quantify the epigenomic status of TEs across human anatomy and development using data from the Roadmap Epigenomics Project. We find that TEs encompass a quarter of the human regulatory epigenome, and 47% of elements can be in an active regulatory state. We demonstrate that SINEs are enriched relative to other classes for active and transcribed marks, that TEs encompass a higher proportion of enhancer states in the hematopoietic lineage, and that DNA methylation of Alu elements decreases with age, corresponding with a loss of CpG islands. Finally, we identify TEs that may perform an evolutionarily conserved regulatory function, providing a systematic profile of TE activity in normal human tissue.
Highlights
Transposable elements (TEs) have deposited functional regulatory elements throughout the human genome
High-level epigenetic profile of TEs across human tissues, we first identified the total proportion of TE bases or CpGs annotated with each epigenetic state across all Roadmap epigenomes (Fig. 1a; Supplementary Fig. 1)
A higher proportion of the LTR class is annotated with the 9_Het heterochromatin state, but the SINE class is more hypermethylated than other classes, suggesting that the two classes are subject to different mechanisms of epigenetic repression
Summary
Transposable elements (TEs) have deposited functional regulatory elements throughout the human genome. Certain TE subfamilies (a collection of TE copies that descended from a single insertion into the ancestral genome) have been co-opted to rewire gene regulatory networks involved in pregnancy and innate immunity[9,10], and they help disseminate CTCF (CCCTC-binding factor) binding sites and establish chromatin boundaries[11,12]. They can act as tissuespecific enhancers[1], in addition to their extensive contributions to the transcriptome in both normal and diseased tissues[13,14]. This dataset has been used to explore the cis-regulatory activity of TEs across tissues[20], a thorough profile of TE contribution to gene regulation across multiple phylogenetic resolutions, using complementary epigenetic measurements, and in rarely profiled tissues is not yet complete
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