TABLE 3.
Non-B DNA and TE integration preferences with the sign of non-B DNA predictors in regression models and the genomic window size (when relevant) used for the analysis (after [91–93]).
| TE/Non-B DNA type | L1s | DNA transposons* | Human and mouse ERVs** |
|---|---|---|---|
| A-phased repeats | Positive for fixation (±50 kb) | Negative for Charlie distributions (1 Mb and 20 kb) | |
| Direct Repeats | Functional negative predictor for fixation | Positive for Tigger distributions (20 kb) | |
| Positive for Helitron distributions (1 Mb) | |||
| G4s | Positive for integration (±2 kb), negative for fixation (±50 kb) | Negative for Tigger distributions (20 kb) | Functional negative predictor of fixed HERV-K distributions |
| Negative for PiggyBat integrations (20 kb) | |||
| Negative for SB integrations (20 Kb) | |||
| Positive for Helitron distributions (1Mb) | |||
| Inverted Repeats | Negative for Charlie distributions (1 Mb) | ||
| Positive for SB integrations (1 Mb) | |||
| Positive for hAT distributions (20 kb) | |||
| Positive for TcMar distributions (20 kb) | |||
| Positive for Helitron distributions (20 kb) | |||
| Mirror Repeats | Positive for integration (−2 kb - insertion), positive for fixation (insertion - 1 kb) | Negative for Charlie distributions (20 kb) | Functional positive predictor of fixed ETn distributions |
| Negative for Tigger distributions (20 kb) | |||
| Negative for PiggyBat integrations (1 Mb) | |||
| Positive for SB integrations (20 kb) | |||
| Negative for hAT distributions (1 Mb) | |||
| Positive for Helitron distributions (1 Mb) | |||
| Z-DNA | Positive for hAT distributions (1 Mb and 20 kb) | Negative scalar predictor for fixed ETn vs. controls distributions | |
| Negative for Helitron distributions (1 Mb) |
*
only predictors with RCVE >1% are shown
**
only predictors with RCDE>1% in multiple functional regression models are shown
***
SB - Sleeping Beauty