Table 1 Intersection of RepeatMasker defined reference genome (hg38) ERV sequences with ENCODE candidate cis-regulatory elements [2]. Values in brackets represent fold-change compared to random sampling, with bold font highlighting > 50% depletion (italicized) or enrichment (underlined). CTCF-bound elements have predicted insulator or looping function
From: Endogenous retroviruses in the origins and treatment of cancer
Family | Reference genome (%) | Promoter (%, n = 60,338) | Proximal enhancer (%, n = 141,830) | Distal enhancer (%, n = 667,599) | CTCF-bound (%, n = 56,766) |
|---|---|---|---|---|---|
ERV | 8.860 | 8.472 (1.0) | 6.124 (0.7) | 12.786 (1.4) | 17.317 (2.0) |
LTR5Hs (HERV-K) | 0.019 | 0.008 (0.4) | 0.032 (1.6) | 0.037 (1.9) | 0.014 (0.7) |
LTR7 (HERV-H) | 0.031 | 0.028 (0.9) | 0.054 (1.7) | 0.118 (3.9) | 0.037 (1.2) |
LTR17 (HERV-W) | 0.016 | 0.017 (1.1) | 0.008 (0.5) | 0.012 (0.8) | 0.012 (0.8) |