Review
Copyright ©The Author(s) 2015.
World J Virology. Aug 12, 2015; 4(3): 219-244
Published online Aug 12, 2015. doi: 10.5501/wjv.v4.i3.219
Table 1 Canonical histone modifications implicated in TGS and TGA
Histone residueModificationFunctionWritersErasersReadersReviewed in
H3K4AcTranscription activation[228]
me1 (enhancer sequences)me2/me3 (regulatory elements at the 5' end of active genes, and in poised genes)Transcription activationTranscription activation, resolution of bivalency from poised genesSET1 (tri)[229], SET7 (mono)[230], MLL[231], SMYD2[232]LSD1 (mono and di)[233], JARID1A/KDM5A JARID1B/KDM5B (di and tri)[234]CHD1[235], RAG2[236], TAF3[237], BPTF[238], BHC80[239], ING FAMILY[240], PYGO2[241][166,242]
H3T6PhosphorylationTranscription activationPKC BLSD1[243]
H3K9Acme1/me2me3 (non-genic regions, centromeric heterochromatin, satellite sequences, long terminal repeats)Transcription activation, histone depositionGCN5/PCAF[244]SIRT6[245]BRD4[246][247]
Transcritional silencing, heterochromatinSUV39H1/2[143], G9a[248], SETDB1[249]JMJD1A/KDM3A[250], JMJD1B/KDM3B[251], JMJD1C/TRIP8, JMJD2A/KDM4A (B/C/D)[252]HP1[253], EED 17406994), TDRD7[254], MPP8[255], UHRF1/2[256], GLP[248], CDY FAMILY[257]
H3K27me1/me2/me3, heterochromatin and facultative heterochromatinTranscritional silencing, heterochromatin, poised genesEZH2, EZH1[258]JMJD1A/KDM3A, JMJD1B/KDM3B, KDM6A/UTX, JMJD3/KDM68, JMJD3/KDM6B[259]Cbx proteins[165], EED[260][166,261]
H3K36AcTranscription activationGCN5, PCAF[244][262]
me1/me2 (in the body and 3' end of genes)me2/me3 (gene bodies)Transcription elongationNSD1, NSD2[263], SET2[264], SMYD2[232], MMSET[265]ASH1[266], JHDM1[267], JHDM1A/KDM2A, JHDM1B/KDM2B[268]ISW1B[269]
H4K20me1 me2me3 (non-genic regions, centromeric heterochromatin, satellite sequences, long terminal repeatsTranscritional silencing, heterochromatin, repression of proinflammatory genesPR-SET7/SET8[270] SUV420H1, SUV420H2[274]SUV420H2[274], SMYD5[275]PHF8[271]PHF2[275]PHF2[275]L3MBTL1[272]PHF20[276], L3MBTL1[277]NcoR[275][273]
Table 2 Coordinates of transcription factor binding sites in the HIV-1 5’LTR
NamePosition1FunctionCell typeNotesRef.
Nuc-0About 40-200StructuralConsistent across different cell typesStable. Stability seems independent of transcription[278]
AP-1/COUP-TFAbout 103Activation/Repression[279]
c-myc/RBF-2 (USF1/2)118-124Repression/ActivationHeLa-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-TFAbout 135Repression/ActivationCell type variationCOUP-TF binds to the nuclear responsive element[180,279]
NFAT173ActivationConsistent across different cell linesNFAT consensus sequence TGGAAA maps on antisense strand[282]
GRE-I192-197Repression/ActivationCell type variationGRE-like element AGAACA[283-285]
AP-1About 208AP-1 recently found to be crucial for latency[286]
YY1/RBF-2About 336Repression/ActivationJurkat, HeLaPutative E-box element RBEIII. Sequence overlaps YY1, RBF-2/TFII-I and AP-1 binding sites[281,287,288]
NFAT/NF-kB350Activation/RepressionConsistent across different cell typesTwo 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-2About 388Activation/RepressionMicroglial, Oligodendrocytes, T lymphocytesCOUP-TF synergises and interacts with SP1 to activate, while CTIP2 directly binds to SP1 and represses transcription[279,292,293]
Nuc-1450-610StructuralConsistent across different cell typesThis nucleosome is remodelled to induce HIV latency or transcriptional gene silencing[278]
RBF-2/AP-4435-440Activation/RepressionHEK293T, JurkatBoth bind the E-box element CAGCTG, which has been named RBEI[288,294-296]
GRE-II450-455Activation/RepressionCell type variationGRE-like element TGTACT[283-285]
LSF/YY1about 440-483RepressionHeLaLSF recruits YY1. This interaction recruits HDCA1 to initiate repression[281,297,298]
GRE-III471-476Repression/ActivationCell type variationGRE-like element AGACCA[283-285]
COUP-TF/AP-1/SP3About 485Repression/ActivationMicroglialSynergises and interacts with SP3[180,279]
RBF-2About 576Activation/RepressionJurkatBinds an atypical RBEIII element: ACTGCTGA[288,294]
NFAT618ActivationConsistent across different cell linesNFAT consensus sequence TGGAAA maps on sense strand[291]