Table 1.
Case examples of TEs functioning as cis-regulatory DNA elements.
| Species | Gene product | TE | Cis-regulatory activity | Function | Evidence | References |
|---|---|---|---|---|---|---|
| Tetrapod vertebrates | ISL1 | LF-SINE (vertebrate SINE) | Neural enhancer | Brain development (inferred) | Sequence conservation, mouse reporter assay | 60 |
| Human | AIM2 | MER41 (primate ERV) | Interferon-inducible enhancer | Regulates inflammatory response | CRISPR knockout in human cell culture | 44 |
| Human | β-globin | ERV9 (primate ERV) | Erythroid enhancer | Controls developmental switch from fetal to adult globin | Cre-LoxP knockout in transgenic mouse BAC, chromatin looping (3C) | 182 |
| Mouse | Dicer | MT-C (rodent LTR retrotransposon) | Oocyte-specific promoter | Necessary for female oocyte function and fertility | TALEN knockout in mouse | 75 |
| Mouse | Growth Hormone | B2 SINE (mouse retrotransposon) | Insulator | Developmental regulation of growth hormone (inferred) | Enhancer blocking assay | 183 |
| Human | Prolactin | MER39 (ERV) | Endometrial-specific promoter | Prolactin expression during pregnancy | 5′ RACE on endometrial tissue | 184 |
| Fly (D. melanogaster) | Cyp6g1 | Accord (LTR retrotransposon) | Enhancer | Increased resistance to DDT insecticide | Selective sweep, genetic mapping, reporter assay | 185 |
| Fly (D. melanogaster) | Jheh1/2 | Bari1 | Antioxidant response elements (enhancer) | Increased resistance to oxidative stress | Selective sweep, phenotypic assays | 186 |
| Fly (D. simulans) | Slowpoke | Shellder (LTR retrotransposon) | Altered splicing | Courtship song variation | Trait mapping, in vivo CRISPR knockout | 187 |
| Maize | TB1 | Hopscotch (teosinte LTR retrotransposon) | Enhancer | Apical dominance branching pattern | Trait mapping, reporter assay in maize leaf protoplast | 77 |
| Sicilian blood orange | Ruby | Tcs1 (LTR retrotransposon) | Cold-responsive promoter | Required for cold-induced accumulation of anthocyanin | Trait mapping, 5′ RACE | 78 |
Further examples can be found in the Catalogue of genes affected by TEs (C-GATE) https://sites.google.com/site/tecatalog/ (Ref 36). 3C, chromatin conformation capture; BAC, bacterial artificial chromosome; ERV, endogenous retrovirus; LF-SINE, living-fossil SINE; LTR, long terminal repeat; RACE, rapid amplification of cDNA ends; SINE, short interspersed nuclear element; TALEN, transcription activator-like effector nuclease.