The cell biology of HIV-1 latency and rebound

Retrovirology

Table 1 Epigenetic factors known to have a repressive or activator role in regulating HIV-1 transcription in T cells and/or microglia

Epigenetic factor		Identified HIV-1 transcriptional regulatory function by cell type
Repressive epigenetic enzymes	Histone or DNA modification	Primary T cells	Transformed T cells	Primary microglia	Transformed microglia	Selected references
HDAC1, 2, and 3	Deacetylation of multiple H3 and H4 sites	+	+	+	+	[135, 139, 416,417,418]
EZH2 (PRC2)	H3K27me3	+	+	+	+	[129, 135, 419]
EHMT2 (G9a)	H3K9me2	+	+	+	+	[129, 419]
SUV39H1	H3K9me3	+	+	?	+	[129, 144, 148, 420]
SMYD2	H4K20me1	+	+	?	?	[147]
DNMT1; DNMT3a	meCpG	+	+	?	?	[130, 157, 163]
LSD1		?	+	?	+	[304, 421]
KAT5 (Tip60)	H4K5Ac, H4K8Ac, H4K12Ac	+	+	?	?	[315]

Activating epigenetic enzymes	Histone or Tat modification
CBP/p300	H3K27Ac and other H3 and H4 acetylation sites; Tat K50Ac and K51Ac	+	+	+?	+?	[134, 135, 418, 422, 423]
GCN5	Primarily H3K14Ac; Tat K50Ac and K51Ac	+?	+?	+?	+?	[290, 418, 423]
PCAF	H3K9Ac, H3K14Ac; H4K8Ac; Tat K28Ac	+?	+?	+?	+?	[291, 418, 423]
UTX/KMD6A	Demethylation of H3K27me3	+	+	?	?	[130]

Epigenetic mediators	Associated partners or complex
Nurr1	CoREST, HDAC1, G9a, EZH2	−	−	+	+	[419]
CTIP2	LSD1, HIC1, HMGA1, HDAC1, HDAC2, SUV39H1, HP1-γ	−	−	?	+	[140, 420, 421, 424]
MBD2	NuRD	+	+	?	?	[157]
SWI/SNF	BAF and PBAF	+	+	?	?	[124,125,126,127,128]
CHAF1a	CAF1	+	+	?	?	[150]
CBX4	PRC1	+	+	?	?	[153]
PML	PML-G9a	+	+	?	?	[154]

(+) indicates evidence of HIV-1 regulatory function by cell type. For the histone acetyltransferases, (+) is a direct demonstration of function based on ChIP assays showing recruitment to the HIV-1 LTR. By contrast, (+?) indicates indirect evidence of possible histone acetyltransferase function based on experimental work conducted using HDAC inhibitors. (−) indicates evidence that the factor either does not participate in or has a non-essential HIV-1 regulatory function in that cell type. (?) indicates that HIV-1 regulatory function is yet to be demonstrated in that cell type

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