Table 2.
Genomic data available for comparison to HIV integration sites
| Group | Type | Source | Number | Types |
|---|---|---|---|---|
| T cell expression |
RNA-Seq |
Unpublished |
1 |
RNA |
| Jurkat expression |
RNA-Seq |
Encode [31] |
1 |
wgEncodeHudsonalphaRnaSeq |
| Integration sites |
Locations |
Unpublished |
1 |
Sites |
| DNase sensitivity |
DNA-Seq/peaks |
Encode [31] |
1 |
wgEncodeOpenChromDnase |
| Methylation |
DNA-Seq |
[32] |
1 |
Methyl |
| CpG |
Locations |
UCSC [33] |
1 |
cpgIslandExt |
| Sequence-based |
Continuous |
— |
4 |
% GC, HIV PWM score, distance to centrosome, chromosomal position |
| Repeats |
Locations |
UCSC [33] |
16 |
DNA, LINE, Low_complexity, LTR, Other, RC, RNA, rRNA, Satellite, scRNA, Simple_repeat, SINE, snRNA, srpRNA, tRNA, alphoid |
| Histone acetylation |
ChIP-Seq/Peaks |
[34] |
18 |
H2AK5ac, H2AK9ac, H2BK120ac, H2BK12ac, H2BK20ac, H2BK5ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac, H3K36ac, H3K4ac, H3K9ac, H4K12ac, H4K16ac, H4K5ac, H4K8ac, H4K91ac |
| Histone methylation and other proteins |
ChIP-Seq/Peaks |
[35] |
23 |
CTCF, H2AZ, H2BK5me1, H3K27me1, H3K27me2, H3K27me3, H3K36me1, H3K36me3, H3K4me1, H3K4me2, H3K4me3, H3K79me1, H3K79me2, H3K79me3, H3K9me1, H3K9me2, H3K9me3, H3R2me1, H3R2me2, H4K20me1, H4K20me3, H4R3me2, PolII |
| Chromatin state |
Binary |
[59] |
51 |
State1,state2,…,state51 |
| HATs and HDACs |
ChIP-Seq |
[36] |
11 |
Resting-HDAC1, Resting-HDAC2, Resting-HDAC3, Resting-HDAC6, Resting-p300, Resting-CBP, Resting-MOF, Resting-PCAF, Resting-Tip60, Active-HDAC6, Active-Tip60 |
| Nucleosome |
ChIP-Seq |
[37] |
2 |
Resting-Nucleosomes, Active-Nucleosomes |
| UCSC genes | Locations | [38] | 4 | In gene, in gene (same strand), gene count, distance to nearest gene, in exon, in intron |