Table 2. Relative enrichment (+) or under-representation (−) of specific repeat families in collections of ZSCAN5, RPC155, TFIIIC, and ETC ChIP peaks.
| Repeat Family1 | ZSCAN5B2 | ZSCAN5A | ZSCAN5D | RPC1553 | TFIIIC3 | ETC3 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| +/− | p-value | +/− | p-value | +/− | p-value | +/− | p-value | +/− | p-value | +/− | p-value | |
| tRNA | + | 0 | + | 0 | + | 0 | + | 0 | + | 0 | ||
| RNA | + | 1.4e-12 | + | 1.5e-02 | ||||||||
| scRNA | + | 1.9e-08 | + | 2.9e-19 | + | 4.3e-02 | ||||||
| snRNA | + | 4.8e-04 | + | 5.3e-14 | ||||||||
| Alu | - | 2.2e-08 | - | 4.3e-25 | - | 7.9e-70 | + | 0 | + | 0 | + | 0 |
| L2 | - | 2.3e-04 | + | 7.7e-10 | - | 1.2e-02 | + | 4.2e-47 | + | 6.4e-70 | ||
| MIR | - | 3.5e-03 | + | 1.2e-171 | + | 4.1e-21 | + | 3.1e-03 | + | 5.7e-04 | ||
| ERV1 | - | 5.0e-03 | - | 5.0e-04 | - | 2.5e-14 | + | 3.3e-07 | - | 1.8e-10 | - | 3.7e-06 |
| telo | + | 7.5e-08 | ||||||||||
| Simple_Repeat | - | 4.1e-04 | - | 1.9e-04 | + | 1.9e-03 | ||||||
| srpRNA | + | 2.3e-02 | + | 1.1e-03 | ||||||||
| Gypsy | + | 2.7e-02 | - | 4.7e-02 | + | 3.4e-22 | ||||||
| Low_Complexity | + | 4.4e-23 | - | 1.4e-06 | + | 1.5e-50 | ||||||
| LTR? | + | 4.8e-10 | ||||||||||
| Deu | + | 3.1e-02 | ||||||||||
| LTR | + | 9.7e-03 | ||||||||||
| rRNA | + | 0 | + | 0 | + | 1.8e-07 | ||||||
| RTE-BovB | + | 2.2e-03 | ||||||||||
| SINE | + | 2.3e-02 | ||||||||||
1
Repeat family names and locations taken from repeat masker,http://www.repeatmasker.org/; a full accounting with enrichments and depletions for specific elements in each family is provided in Supplementary Table 3.
2
ChIP peaks from the BeWo cell line, focused on all fdr=0 peaks (ZSCAN5B) or all peaks with enrichment > 15 for ZCAN5A and ZSCAN5D, as reported in Supplementary Table 2.
3
Peak coordinates for these feature types are taken from [19], and were lifted over to human genome sequence build hg19 for comparisons.