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. 2019 Dec 10;10:5640. doi: 10.1038/s41467-019-13555-x

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a The total number of epigenetic states with which each TE subfamily is annotated across all epigenomes (see Methods; n = 968 TE subfamilies, n = 965 for methylation states). b PCA on Roadmap epigenomes (n = 127 epigenomes), using the LOR enrichment of each TE subfamily in each chromHMM state (13,716 subfamily-by-state combinations) as variables. Color is based on group (see legend above Fig. 5b), and shape is based on epigenome age (non-fetal and unknown age are not distinguished). c PCA on TE subfamilies (n = 937 subfamilies), using the LOR enrichment of the subfamily in each chromHMM state in each Roadmap epigenome (1,904 state-by-epigenome combinations) as variables. Color is based on class (see legend below Fig. 5d), and shape is based on TE family (only Alu and L1 are highlighted). b, c The amount of variation explained by each PC is listed in parentheses. d The proportion of epigenomes each TE subfamily is enriched LOR > 1.5 in the epigenetic state (chromHMM states 127 epigenomes, methylation states 37, DHS 53, H3K27ac 98). Each subfamily is represented by a circle and is colored by TE class (see Methods). The n below each state on the y-axis indicates the number of subfamilies enriched in the state in at least one epigenome. e The percentage of LTR22A elements that contain a binding motif for the transcription factor. Active TEs: elements annotated with the 7_Enh enhancer state in epigenomes where the subfamily is enriched in the state (n = 103 TEs); Inactive TEs: elements never in the state (n = 68 TEs). The top 5 most significant transcription factors as predicted by HOMER are shown (binomial FDR-corrected P-value < 0.0001 for each).