Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus

Table 2 Coordinates of transcription factor binding sites in the HIV-1 5’LTR

Name	Position1	Function	Cell type	Notes	Ref.
Nuc-0	About 40-200	Structural	Consistent across different cell types	Stable. Stability seems independent of transcription	[278]
AP-1/COUP-TF	About 103	Activation/Repression			[279]
c-myc/RBF-2 (USF1/2)	118-124	Repression/Activation	HeLa-CAT-CD4 and J-Lat J89 (Jurkat)	Binds the sequence CACTGAC in HIV promoter, but the canonical sequence is CACGTGAC	[280,281]
				Recruited by Sp1, can bind directly to the promoter to recruit HDAC1
				RBF-2 can potentially bind to the CTGAC of this motif.
AP-1/COUP-TF	About 135	Repression/Activation	Cell type variation	COUP-TF binds to the nuclear responsive element	[180,279]
NFAT	173	Activation	Consistent across different cell lines	NFAT consensus sequence TGGAAA maps on antisense strand	[282]
GRE-I	192-197	Repression/Activation	Cell type variation	GRE-like element AGAACA	[283-285]
AP-1	About 208			AP-1 recently found to be crucial for latency	[286]
YY1/RBF-2	About 336	Repression/Activation	Jurkat, HeLa	Putative E-box element RBEIII. Sequence overlaps YY1, RBF-2/TFII-I and AP-1 binding sites	[281,287,288]
NFAT/NF-kB	350	Activation/Repression	Consistent across different cell types	Two shared in-tandem binding sites for each transcription factor. NF-kB in the sense strand, NFAT in the antisense	[289-291]
COUP-TF/Sp1/CTIP-2	About 388	Activation/Repression	Microglial, Oligodendrocytes, T lymphocytes	COUP-TF synergises and interacts with SP1 to activate, while CTIP2 directly binds to SP1 and represses transcription	[279,292,293]
Nuc-1	450-610	Structural	Consistent across different cell types	This nucleosome is remodelled to induce HIV latency or transcriptional gene silencing	[278]
RBF-2/AP-4	435-440	Activation/Repression	HEK293T, Jurkat	Both bind the E-box element CAGCTG, which has been named RBEI	[288,294-296]
GRE-II	450-455	Activation/Repression	Cell type variation	GRE-like element TGTACT	[283-285]
LSF/YY1	about 440-483	Repression	HeLa	LSF recruits YY1. This interaction recruits HDCA1 to initiate repression	[281,297,298]
GRE-III	471-476	Repression/Activation	Cell type variation	GRE-like element AGACCA	[283-285]
COUP-TF/AP-1/SP3	About 485	Repression/Activation	Microglial	Synergises and interacts with SP3	[180,279]
RBF-2	About 576	Activation/Repression	Jurkat	Binds an atypical RBEIII element: ACTGCTGA	[288,294]
NFAT	618	Activation	Consistent across different cell lines	NFAT consensus sequence TGGAAA maps on sense strand	[291]

¹Genomic coordinates are based on the HBX2 numbering system. Nuc-0: Nucleosome 0; AP-1: Activator protein 1; COUP-TF: Chicken ovalbumin upstream transcription factor; c-myc: V-myc avian myelocytomatosis viral oncogene homolog; RBF-2: Ras-responsive binding factor 2; USF1/2: Upstream stimulatory factor 1 or 2; NFAT: Nuclear factor of activated T cells; GRE-I: Glucocorticoid responsive element I; YY1: Ying-yang 1; NF-κB: Nuclear factor kappa beta; Sp1: Specificity protein 1; CTIP-2: COUP-TF interacting protein 2; Nuc-1: Nucleosome 1; AP-4: Activator protein 4; GRE-II: Glucocorticoid responsive element II; Sp3: Specificity protein 3.