Table 4.
Compilation of bisulfite treatment and sequencing results.
| Probe set | Baseline expression value | Fold change | p-value | Annotation | Promoter region | Coding region | ||
| Total bp analyzed | # methylated cytosines/# total cytosines | Total bp analyzed | # methylated cytosines/# total cytosines | |||||
| Control genes | ||||||||
| 64.m00187 | 14.05 | 0.90 | 0.731 | Hsp100 | 455 | 10/62 | 397 | 48/48 |
| 64.m00187** | 14.05 | 0.90 | 0.731 | Hsp100** | ND | ND | 397 | 0/48 |
| Significantly upregulated | ||||||||
| 141.m00082 | 0.32 | 2.98 | 0.010 | protein kinase, putative | 308 | 36/36 | 73 | 13/13 |
| 115.m00143 | 0.12 | 3.64 | 0.001 | transcription initiation factor TFIID, putative | 266 | 0/27 | 254 | 5/40 |
| 97.m00140_at | 0.08 | 3.10 | 0.006 | hypothetical protein | 248 | 59/59 | 110 | 23/23 |
| Marginally upregulated | ||||||||
| 687.m00016_at | 12.16 | 18.68 | 0.091 | hypothetical protein | 328 | 18/18 | ND | ND |
| 3.m00674_at | 0.62 | 2.17 | 0.089 | hypothetical protein | 143 | 16/16 | ND | ND |
| 160.m00098_at | 11.46 | 1.72 | 0.112 | hypothetical protein | 244 | 16/16 | ND | ND |
| 26.m00304_at | 0.54 | 1.64 | 0.086 | hypothetical protein | 115 | 19/19 | ND | ND |
| Significantly downregulated | ||||||||
| 226.m00092_at | 0.343 | 0.34 | 0.008 | Rab family GTPase | 347 | 0/27 | 41 | 0/6 |
64.m00187_s_at also represents 111.m00116, 181.m00064, 192.m00086, 365.m00018, 482.m00014, 493.m00033, 511.m00026, 82.m00144, and 872.m00009.
The probe set, baseline expression value in E. histolytica HM-1:IMSS trophozoites, fold change, p-value, and gene annotation are shown. For each gene the number of base pairs analyzed, the number of methylated cytosines, the number of total cytosines analyzed, and the location (promoter or coding region) are indicated. Genomic DNA from E. histolytica HM-1:IMSS parasites was treated with 10 M sodium bisulfite and PCR amplified. Six independent clones were analyzed for each region of interest to determine the extent of cytosine methylation; for a particular cytosine position to be indicated as methylated 4 out of 6 clones had to be methylated. ** represents genomic DNA from E. histolytica HM-1:IMSS parasites treated with 23 μM 5-AzaC for 7 days. ND = not done. Primers used in PCR analysis of the Hsp100 gene were specific to 192.m00086 and were identical to those used by Bernes et al. [16].