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. 2004 Jun;78(12):6122–6133. doi: 10.1128/JVI.78.12.6122-6133.2004

TABLE 1.

Characteristics of HIV-1 integration sites in infected resting CD4+ T cells

Chromosome Patient identification no. Junctional sequencea Chromosome locus Host nt at the junctionb Integration sitec Host gene Description Orientationd nt from host transcription start sitee Host gene expressionf
Resting With PHA
1 21 AAGGTGTTCC 1p36.23 8158129 I RERE Arg-Glu dipeptide (RE) repeats − 428941 (0.92) + +
21 AAGGTTGCCA 1p36.22 9744195 I NMNAT1 Nicotinamide adenylyltransferase + 31162 (0.78) + +
149 AAGGTATGAG 1p36.11 23360670 I FUSIP1 FUS-interacting protein 1 − 6447 (0.46) + +
22 AAGGTCCAAC 1p34.3 35378363 I PKD1-like Polycystic kidney disease 1 related + 72287 (0.59) + +
21 AAGGTGAGGG 1p34.3 35405894 I PKD1-like Polycystic kidney disease 1 related − 44772 (0.36) + +
150 AAGGTCTATA 1p31.3 64357286 I KIAA1573 Unknown function − 15771 (0.08) + +
144 AAGGTCTAAT 1q21.3 151082976 I p66beta Transcription repressor p66 beta − 29040 (0.25) + +
153 AAGGTTCTCC 1q22 151774696 I ADAR Adenosine deaminase, RNA isoform + 22765 (0.87) + +
143 AAGGTCAGAA 1q32.1 196246333 Int
2 153 AAGGTGGTTC 2p23.2 28443777 I BRE Brain and reproductive organ expressed + 355646 (0.79) + +
153 AAGGTGAGTC 2q37.3 241972574 I Predictedg − 22723 (0.89) − −
3 21 AAGGTTAATC 3p24.1 30695399 I TGFBR2 Transforming growth factor β receptor II − 72396 (0.85) + +
21 AAGGTTACAC 3p21.31 49514417 I DAG1 Dystroglycan 1 precursor + 47814 (0.73) + +
21 AAGGTAGAGG 3q29 198226821 I DLG1 Synapse-associated protein 97 − 125147 (0.49) + +
4 21 AAGGTATATG 4p14 38495952 I Predictedg − 37220 (0.69) − −
21 AAGGTCAAAA 4q25 111007127 I FLJ20647 Hypothetical protein − 66890 (0.52) + +
5 103 AAGGTTGACG 5q11.2 54977619 I FLJ90709 Hypothetical protein − 46361 (0.54) + +
21 AAGGTTATTC 5q15 96212730 E ARTS-1 Aminopeptidase regulator of shedding + 4985 (0.11) + +
142 AAGGTGCATA 5q23.1 121481991 E LOX Lysyl oxidase preproprotein − 8154 (0.68) − −
21 AAGGTTATGT 5q23.2 127559778 I SLC12A2 Solute carrier family 12 − 64079 (0.62) + +
22 AAGGTCGTAC 5q31.3 139878769 I FLJ20288 Hypothetical protein − 68775 (0.47) + +
6 21 AAGGTAATTG 6p25.1 5551277 I FARS1 Phenylalanine-tRNA synthetase + 237482 (0.59) + +
144 AAGGTCAGAA 6p21.33 30612175 I Predictedg + 48696 (0.89) + +
144 AAGGTGATGG 6p21.32 32940155 I TAP2 TAP2 + 203049 (0.68) + +
79 AAGGTGACAC 6p21.31 35693844 I FKBP51 FK506-binding protein 51 + 9725 (0.09) + +
21 AAGGTTGTAA 6p21.2 38617237 I BTBD9 KIAA1880 protein − 37208 (0.08) + +
21 AAGGTTTTTG 6q23.3 135304182 I HBS1L HBS1-like − 52410 (0.55) + +
21 AAGGTGATCC 6q23.3 135501140 I MYB v-myb myeloblastosis homolog + 18030 (0.48) + +
22 AAGGTTGATA 6q23.3 135792304 I FLJ20069 Hypothetical protein + 7149 (0.03) − −
7 21 AAGGTAATAT 7q22.3 106071860 I PIK3CG Phosphatidylinositol 3-kinase, catalytic, gamma + 5405 (0.13) + +
8 21 AAGGTGGGTA 8q24.3 144830024 E hmRNAh + 935 (0.28) + +
9 22 AAGCTGCAGC 9q21.2 75991003 I GNAQ GTP-binding protein, q protein + 112487 (0.36) + +
22 AAGGTTACCG 9q32 112854741 I Predictedg + 46833 (0.43) − −
10 21 AAGGTAAGGA 10q25.1 111475750 I ADD3 Adducin 3 isoform a − 45357 (0.35) − −
11 21 AAGGTAAAAA 11p15.4 9744195 I NAP1L4 Nucleosome assembly protein − 7800 (0.16) + +
21 AAGGTCACAG 11q13.1 64319021 I SF1 Splicing factor 1 − 2574 (0.18) + +
21 AAGGTATTAT 11q13.4 71857871 I SKD3 Suppressor of K transport defect 3 + 14005 (0.10) + +
12 143 AAGGTCGATT 12p13.32 3825992 I c12orf6 Chromosome 12 open reading frame 6 + 26809 (0.44) + +
152 AAGGTCAAAG 12p11.21 31748771 I hmRNAh + 24508 (0.42) − +
150 AAGGTGAAAC 12q13.12 49358494 I FLJ34278 Hypothetical protein − 173459 (0.99) + +
151 AAGGTGTCGA 12q13.13 52922906 I CBX5 Heterochromatin protein 1 + 16679 (0.93) + +
145 AAGGTAATGG 12q22 91298430 I Predictedg + 47946 (0.32) − −
15 146 AAGGTCACTC 15q22.2 57090553 I RNF111 Ring finger protein 111 − 94632 (0.87) + +
21 AAGGTGAATC 15q23 66135863 I PIAS1 Inhibitor of activated STAT + 73473 (0.55) + +
153 AAGGTTATAG 15q25.3 83919694 I AKAP13 A-kinase (PRKA) anchor protein 13 − 266055 (0.72) + +
16 153 AAGGTTTTTC 16p11.2 29719156 I hmRNAh + 522325 (0.81) − −
21 AAGGTTCCGA 16p11.2 29762139 I hmRNAh − 479342 (0.74) − −
21 AAGGTGAGAA 16p11.2 29847207 I KIF22 Kinesin family member 22 − 7512 (0.51) + +
21 AAGGTCATTG 16q13 57040912 I hmRNAh +
79 GAGGTTTTAG 16q22.1 67956187 I NFATc3 Nuclear factor of activated T cells + 60576 (0.43) + +
17 21 AAGGTGTCAG 17p13.3 2435251 E FLJ10543 Hypothetical protein − 10740 (0.80) + +
21 AAGGTGAAAG 17p11.2 16262774 I NCoR1 Nuclear receptor corepressor 1 − 56637 (0.31) + +
21 AAGGTGGAGG 17p11.2 20012102 I AKAP10 A-kinase anchor protein 10 + 31056 (0.43) + +
150 AAGGTGGACC 17p21.2 38936487 I TOP2A DNA topoisomerase II alpha + 10739 (0.38) − +
103 AAGGTGGTTT 17q21.31 42202698 I MEOX1 Mesenchyme homeobox 1 + 11398 (0.54) − +
21 AAGGTGAAAG 17q25.1 73929654 I GRB2 Growth factor receptor-bound 2 − 57225 (0.78) + +
21 AAGGTCACTT 17q25.1 74812346 I hmRNAh,i − + +
153 AAGGTGAAGG 17q25.1 74938954 I PRPSAP1 PRPP synthetase associated − 8100 (0.19) + +
153 AAGGTGACTG 17q25.3 76515866 I EVER1 Epidermodysplasia verruciformis 1 + 206035 (0.55) + +
21 AAGGTCAGGC 17q25.3 80511487 Int LINE (L1)
20 AAGGTGGATC 17q25.3 81407969 I TBCD β-Tubulin cofactor D − 19195 (0.10) + +
19 99 AAGGTCTCTA 19p13.2 10153709 I DNMT1 DNA methyltransferase 1 + 13102 (0.21) + +
21 AAAGTGATCC 19p13.2 10309206 I ICAM3 Intercellular adhesion molecule 3 + 2094 (0.36) + +
21 AAGGTTATTC 19p13.11 17800839 I JAK3 Janus kinase 3 − 15443 (0.84) + +
22 AAGCTGCAGT 19q13.11 39535086 I KIAA0355 Hypothetical protein + 97769 (0.97) + +
21 AAGGTGGGTC 19q13.12 40889171 Int
152 AAGGTCTACC 19q13.33 55192036 I VRK3 Vaccinia virus-related kinase 3 − 28412 (0.58) + +
21 AAGGTGAGTT 19q13.43 61779316 I Predictedg − 9227 (0.17) + +
20 153 AAGGTGAGGA 20q13.13 50223866 I ADNP Activity-dependent neuroprotector − 9083 (0.22) + −
22 22 AAGGTCAATT 22q11.21 19609567 I CRKL v-crk oncogene homolog + 13299 (0.40) + +
153 AAGGTGAGGA 22q13.1 35834266 Int LTR (endogenous retrovirus 1)
21 AAGGTTAGTG 22q13.1 36501308 I EIF3S6IP Eukaryotic translation initiation factor 3 − 12844 (0.33) + +
22 AAGGTCATGA 22q13.33 49112299 Int Alu
X 22 AAGGTCTAAA Xp11.3 41971993 I Predictedg + 75610 (0.48) − −
a

Junction between the 5′ end of the HIV-1 LTR (first five letters) and the host cell DNA.

b

The host nucleotide number at the junction was determined by using the UCSC Bioinformatics Human Genome Database (July 2003 assembly freeze). Bold type indicates clusters of two integration events within a 1-Mb window (P, 3.9 × 10−5). Italic type indicates clusters of three integration events within a 1-Mb window (P, 2.6 × 10−5).

c

Nature of the integration site: I, intron; E, exon; Int, intergenic. Overall, 93.2% (69 of 74) of the integration sites were in defined or predicted genes, while 6.8% (5 of 74) were in intergenic regions. Among integrations in genes, 94.2% (65 of 69) were in introns and 5.8% (4 of 69) were in exons.

d

Transcriptional orientation: +, the host gene and the HIV-1 insert have the same transcriptional orientation; −, the gene and the insert have the opposite orientation. Of genes in transcription units, 49.3% (34 of 69) were in the + orientation and 50.7% (35 of 69) were in the − orientation.

e

Distance, in nucleotides, between the start site for transcription of the host gene and the HIV-1 integration site. Numbers in parentheses indicate the relative position of the integration site within the gene, with 0 representing the start of transcription and 1 representing the end of the transcript.

f

For integration sites within known or predicted genes, RT-PCR was carried out with gene- specific primers spanning an intron on total RNA isolated from purified resting or activated (with PHA) CD4+ T cells. +, presence of a PCR product of the predicted size; −, no PCR product under conditions that gave a readily detectable band for a ubiquitously expressed gene (GAPDH) and, for characterized genes, a correct product from cell lines or primary tissues known to express the gene. These included chondrocytes (LOX), kidney cells (ADD3), and mesenchymal stem cells (MEOX1). The expression of TOP2A, MEOX1, and a human mRNA from chromosome 12p11.21 was detected in activated but not resting CD4+ T cells. For integration events in well-characterized (RefSeq) genes, expression of the targeted gene in resting CD4+ T cells was observed for 91.1% (51 of 56) of the genes.

g

Gene predicted by the Genscan algorithm.

h

hmRNA, human mRNA from GenBank.

i

The start site for transcription has not yet been determined.