Table 1.
Summary of data on effects on gene-specific methylation of increasing (transgene overexpression) or reducing (siRNA) expression of Sirt1 in Caco-2 cells
| Gene | Region analysed | Number of CpG sites analysed | CpG sites affected by manipulating level of SIRT1 expression | |||
|---|---|---|---|---|---|---|
| CpG number | Methylation (%) in cells with overexpressed SIRT1 | Methylation (%) in control cells | Methylation (%) in cells with reduced SIRT1 expression | |||
| (relative to start of transcription) | (sequential position within region analysed relative to start of transcription) | [median (Q1, Q3); n = 6–9] | [median (Q1, Q3); n = 9–12] | [median (Q1, Q3); n = 12–18] | ||
| CDC7 | −59 to +1 | 8 | 8 | 2.00 (1.50, 2.00) | 2.00 (2.00, 2.00) | 1.50 (0.00, 2.00)* |
| EIF5 | −61 to +1 | 8 | 1 | 1.00 (1.00, 1.50)** | 0.00 (0.00, 0.25) | 0.00 (0.00, 0.25)## |
| 2 | 1.00 (0.00, 1.50)* | 0.00 (0.00, 1.00) | 0.00 (0.00, 0.00)## | |||
| 4 | 2.00 (1.00, 2.50) | 2.00 (2.00, 3.25) | 5.00 (2.00, 8.00)*## | |||
| IRX3 | −65 to +1 | 3 | 1 | 92.00 (91.50, 97.00) | 94.00 (91.75, 95.00) | 91.50 (88.75, 93.00)* |
| 3 | 83.00 (82.00, 87.00) | 86.50 (85.00, 91.00) | 90.00 (87.75, 91.00)## | |||
| KLF3 | −70 to −45 | 6 | 3 | 0.00 (0.00, 1.50)* | 0.00 (0.00, 0.00) | 0.00 (0.00, 0.00) |
| PCYT1A | −89 to +1 | 2 | None affected | |||
| PTPRG | −73 to +1 | 9 | 9 | 7.00 (5.50, 11.50) | 8.00 (5.00, 12.25) | 5.00 (4.00, 6.00)**# |
| SLC39A4 | −92 to +1 | 3 | None affected | |||
| TBX3 | −135 to +1 | 3 | 1 | 96.00 (93.50, 96.50) | 95.00 (85.00, 98.00) | 84.50 (64.75, 92.00)**## |
| 2 | 84.00 (83.00, 87.00) | 83.00 (76.75, 86.00) | 78.50 (61.75, 81.00)**## | |||
| 3 | 91.00 (86.50, 95.00) | 87.00 (79.75, 90.00) | 77.00 (59.50, 82.25)**## | |||
| EIF3L | +22 to +58 | 7 | 1 | 1.00 (0.75, 1.50) | 0.50 (0.00, 1.50) | 0.25 (0.00, 1.00)# |
| 4 | 1.00 (0.25, 1.50) | 1.00 (0.00, 1.75) | 1.75 (1.25, 2.00)# | |||
| PTPRA | −247 to −219 | 4 | 1 | 0.75 (0.50, 0.75)* | 1.00 (0.75, 1.25) | 1.25 (1.00, 1.25)## |
| 2 | 1.50 (1.25, 1.50) | 1.25 (0.50, 1.50) | 1.00 (1.00, 1.25)# | |||
| 3 | 1.75 (1.50, 1.75) | 1.75 (1.50, 2.00) | 2.25 (2.00, 2.50)### | |||
| 4 | 2.75 (2.50, 3.00) | 3.00 (2.75, 3.50) | 3.00 (2.75, 3.75)# | |||
| SP3 | −1,202 to −1,157 | 6 | 4 | 4.25 (3.50, 5.00) | 5.50 (5.00, 6.25) | 5.25 (5.00, 5.75)# |
| STK10 | −100,788 to −100,745 | 6 | 1 | 0.50 (0.00, 0.75) | 0.75 (0.00, 0.75) | 1.00 (0.75, 1.25)*# |
| 2 | 2.00 (1.75, 2.25) | 2.25 (1.75, 2.50) | 2.50 (2.25, 2.75)# | |||
| 4 | 0.50 (0.00, 1.00) | 0.50 (0.00, 1.00) | 1.00 (0.75, 1.25)** | |||
| 5 | 0.00 (0.00, 0.75) | 0.75 (0.00, 1.00) | 0.75 (0.50, 1.25)# | |||
Values for the control condition were derived through combining the data for controls for Sirt1 overexpression (plasmid minus Sirt1 transgene insert) and knockdown (control siRNA), which did not differ. Data are stated only for CpG sites at which significant effects of Sirt1 expression level were measured and are stated to the nearest 0.25 %, based on a calculation of medians and quartiles from values rounded to the nearest 1 %
Q1 first quartile, Q3 third quartile
*p < 0.05; **p < 0.01 compared with control; #p < 0.05; ##p < 0.01; ###p < 0.001 compared with SIRT1 overexpression, by Kruskal–Wallis followed by Dunn’s multiple comparison tests