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. 2022 Apr 14;79:103985. doi: 10.1016/j.ebiom.2022.103985

Table 1.

Most statistically significant 5-AzadC-induced differentially-demethylated CpG dinucleotides (DDMPs).

Cell line CpG positiona Probability of 5-AzadC-induced demethylation p-valueb Statistical-significance Locationc DDMPd
J-Lat 6.3 cells
 -[158,159] 0,33 0,046 * N/A DDMP3
-[96, 97] 0,33 0,0466 * NF-κB site DDMP6
-[74,75] 0,45 0,32 * Sp1 site III DDMP7
-[63,64] 0,42 0,0186 * Sp1 site II DDMP8
-[47, 48] 0,42 0,0186 * Sp1 site I DDMP9
+[109, 110] 0,42 0,0186 * U5 interacting with ψ DDMP10
+[183, 184] 0,42 0,0186 * PBS DDMP11
+[186, 187] 0,33 0,0466 * PBS DDMP12
+[205, 206] 0,42 0,0186 * Interferon-Stimulated Response Element DDMP14
+[243, 244] 0,33 0,0466 * Zinc Knuckles in p7Gag binding to SL1 DDMP17
+[261, 262] 0,42 0,0186 * SL2 of ψ DDMP20
+[278, 279] 0,42 0,0186 * Sp1 site of HSIV DDMP22
+[282, 283] 0,33 0,0466 * Sp1 site of HSIV DDMP23
+[295, 296] 0,33 0,0466 * SL2 of ψ DDMP24
+[314, 315] 0,42 0,0186 * SL3 of ψ DDMP25
+[341, 342] 0,5 0,0069 ** SL4 of ψ DDMP26
+[360, 361] 0,33 0,0466 * Coding sequence of p17Gag DDMP28
+[390, 391] 0,6 0,0167 * Coding sequence of p17Gag DDMP30
J-Lat 8.4 cells
 -[119, 120] 0.64 0.0045 ** CRE site DDMP5
-[96, 97] 0.33 0.0466 * NF-κB site DDMP6
+[183, 184] 0.33 0.0466 * N/A DDMP11
+[205, 206] 0.33 0.0466 * Interferon-Stimulated Response Element DDMP14
+[231, 232] 0.45 0.0320 * N/A DDMP15
+[360, 361] 0.33 0.0466 * Coding sequence of p17Gag DDMP28
J-Lat 15.4 cells -[217, 218] 0.33 0.0466 * N/A DDMP1
-[47, 48] 0.42 0.0186 * Sp1 site DDMP9
+[109, 110] 0.33 0.0466 * U5 interacting with ψ DDMP10
+[205, 206] 0.42 0.0186 * Interferon-Stimulated Response Element DDMP14
+[231, 232] 0.42 0.0186 * N/A DDMP15
+[234, 235] 0.33 0.0466 * SL1 of ψ DDMP16
+[243, 244] 0.33 0.0466 * Zinc Knuckles in p7Gag binding to SL1 DDMP17
+[295, 296] 0.50 0.0069 * SL2 of ψ DDMP24
+[314, 315] 0.33 0.0466 * SL3 of ψ DDMP25
+[341, 342] 0.42 0.0186 * SL4 of ψ DDMP26
+[347, 348] 0.33 0.0466 * SL4 of ψ DDMP27
+[360, 361] 0.36 0.0129 * Coding sequence of p17Gag DDMP28
a

Position given in coordinates where nt+1 is located at the junction U3/R in the 5’LTR.

b

Statistical significance attributed with * for p ≤ 0.05, ** for p ≤ 0.01 and *** for p ≤ 0.001 by [Fisher's exact test].

c

Location of CpG within regulatory or structural elements according to the HIV-1 Database.47,92 N/A refers to no known features.

d

Differentially-Demethylated Position.

DDMPs located in transcription factor binding sites are in bold.