Table 1.
Summary of genomic locations of all sequenced CpG sites and differentially methylated sites (DMSs) between urban and forest great tits in liver and blood*
| Total | Promoter | TSS | Gene body | CGI | CGI shore** | Nonregulatory | |
|---|---|---|---|---|---|---|---|
| Liver | |||||||
| All CpG | 6,166,831 | 2,440,376 (39.6%) | 1,508,486 (25.5%) | 3,961,469 (64.2%) | 3,002,199 (48.7%) | 1,316,950 (21.4%) | 711,340 (11.5%) |
| DMSs | 419 | 93 (22.2%) | 31 (7.4%) | 224 (53.5%) | 208 (49.6%) | 137 (32.7%) | 33 (7.9%) |
| Blood | |||||||
| All CpG | 5,130,570 | 2,197,364 (42.8%) | 1,346,853 (26.3%) | 3,339,042 (65.1%) | 2,882,780 (56.2%) | 1,148,229 (22.4%) | 421,862 (8.2%) |
| DMSs | 1,144 | 173 (15.1%) | 69 (6.0%) | 654 (57.2%) | 417 (36.5%) | 422 (36.9%) | 146 (12.8%) |
Coverage thresholds adopted were 3x for all CpG sites and 10x for DMSs.
Abbreviations: CGI, CpG island; TSS, transcription start site.
*
Note that CpG sites can be associated with one of more genomic features.
**
CGI shores are defined as 2 kb regions flanking CpG islands.