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Table 4 Compilation of bisulfite treatment and sequencing results.

From: Growth of the protozoan parasite Entamoeba histolytica in 5-azacytidine has limited effects on parasite gene expression

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
  1. 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.
  2. 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].
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