Detection, characterization and regulation of antisense transcripts in HIV-1

Landry, Sébastien; Halin, Marilène; Lefort, Sylvain; Audet, Brigitte; Vaquero, Catherine; Mesnard, Jean-Michel; Barbeau, Benoı̂t

doi:10.1186/1742-4690-4-71

Cited by 106 publications

(138 citation statements)

References 42 publications

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“…Importantly, these CTL responses are not limited to ARFs in the sense direction, but may also target antisense-encoded ARFs (5,6). Antisense transcription of known host genes in human and rodent cells has been extensively described (7)(8)(9)(10), and the existence of an antisense protein (ASP) in HIV was first proposed more than 20 years ago (10)(11)(12). The extent to which such viral antisense transcripts encode functional proteins remains largely unknown.…”

Section: Irus-specific Cd8mentioning

confidence: 99%

Immune Screening Identifies Novel T Cell Targets Encoded by Antisense Reading Frames of HIV-1

Berger

Llano

Carlson

et al. 2015

J Virol

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k Cytotoxic-T lymphocyte (CTL) responses to epitopes in alternative HIV reading frames have been reported. However, the extent of CTL responses to putative proteins encoded in antisense reading frames is unknown. Using sequence alignments and computational approaches, we here predict five potential antisense HIV proteins and characterize common CTL responses against them. Results suggest that antisense-derived sequences are commonly transcribed and translated and could encode functional proteins that contain important targets of anti-HIV cellular immunity. V irus-specific CD8ϩ cytotoxic-T lymphocyte (CTL) responses are important in the control of HIV infection (1-3). Accumulating evidence indicates that in addition to CTL responses targeting known structural and nonstructural HIV proteins, CTL responses to epitopes in alternative reading frames (ARFs) of HIV can contribute to in vivo immune selection pressure (4-6). Importantly, these CTL responses are not limited to ARFs in the sense direction, but may also target antisense-encoded ARFs (5, 6). Antisense transcription of known host genes in human and rodent cells has been extensively described (7-10), and the existence of an antisense protein (ASP) in HIV was first proposed more than 20 years ago (10-12). The extent to which such viral antisense transcripts encode functional proteins remains largely unknown.Here, we sought to provide further evidence supporting the existence of fully translated ASPs in HIV by assessing the presence of ASP-specific cellular host immune responses. In a first step, 355 unique full-length HIV-1 clade B sequences were retrieved from the Los Alamos database (13) to generate a consensus sequence for all three antisense reading frames. Five sequences starting with a classical methionine translation start codon followed by Ͼ150 nucleotides without stop codons and with conservation of Ͼ50% (range, 56 to 78%) at all amino acid positions were identified (Fig. 1). The highest conservation scores were obtained for the MAN sequence (entropy score, 0.04; i.e., 99.4% conservation), followed by those for MLK (0.11, 98.2%), MGS (0.18, 97.9%), MPQ (0.16, 97.4%), and the putative MAL protein (0.31, 92.5%). This analysis placed the five ASPs in the range of conservation between the highly conserved HIV p24 (0.21, 99.7%) and the variable Vpu (0.34, 92%) proteins, overall being comparable to other regular reading frame-encoded HIV proteins (14). The ASP sequences ranged from 50 to 179 amino acids in length and included a previously predicted ASP (11). To find immunological evidence that proteins were indeed produced from these antisense open reading frames (ORFs), HIV-infected individuals were tested for T cell responses against corresponding consensus overlapping peptide (OLP) sets by gamma interferon (IFN-␥)-enzyme-linked immunosorbent spot (ELISpot) assay (4) (see Table 1 in the supplemental material). A total of 60 HLA-typed individuals, including 40 chronically HIV-infected subjects and 20 HIV-uninfected controls, were tested. Responses to the A...

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Section: Irus-specific Cd8mentioning

confidence: 99%

Immune Screening Identifies Novel T Cell Targets Encoded by Antisense Reading Frames of HIV-1

Berger

Llano

Carlson

et al. 2015

J Virol

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“…HIV-1 | asp and env genes | overlapping genes | phylogenetic analyses | selection pressure I t is well established that retroviruses are able to perform antisense transcription from the 3′ long terminal repeat (LTR) of their proviral genome (1,2). In 1988, the existence of an ORF on the antisense strand of the HIV type 1 (HIV-1) genome was suggested (3).…”

mentioning

confidence: 99%

“…The existence of this ORF and of the encoded protein was controversial for many years, but now several pieces of evidence argue in favor of its expression (see ref. 4 for an extensive review): (i) several polyadenylated antisense transcripts capable of encoding ASP have been characterized within HIV-1-infected cells (1,5,6); (ii) it was demonstrated that the full-length ASP protein can be expressed ex vivo from the HIV-1 3′ LTR (7); (iii) ASP has been detected in freshly infected cells (2,8,9); and (iv) two recent independent clinical studies have shown the in vivo expression of ASP by detecting a cell-mediated immune response against several ASP epitopes within 30% of individuals infected with subtype B viruses (10,11) [a percentage similar to those observed with other HIV-1 proteins, e.g., Tat and Pol (12)]. Moreover, experimental results suggested that ASP could form stable aggregates, be located partially at the plasma membrane, and be associated with autophagy (4,7,8).…”

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confidence: 99%

Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic

Cassan

Arigon-Chifolleau

Mesnard

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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114

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Recent experiments provide sound arguments in favor of the in vivo expression of the AntiSense Protein (ASP) of HIV-1. This putative protein is encoded on the antisense strand of the provirus genome and entirely overlapped by the env gene with reading frame −2. The existence of ASP was suggested in 1988, but is still controversial, and its function has yet to be determined. We used a large dataset of ∼23,000 HIV-1 and SIV sequences to study the origin, evolution, and conservation of the asp gene. We found that the ASP ORF is specific to group M of HIV-1, which is responsible for the human pandemic. Moreover, the correlation between the presence of asp and the prevalence of HIV-1 groups and M subtypes appeared to be statistically significant. We then looked for evidence of selection pressure acting on asp. Using computer simulations, we showed that the conservation of the ASP ORF in the group M could not be due to chance. Standard methods were ineffective in disentangling the two selection pressures imposed by both the Env and ASP proteins-an expected outcome with overlaps in frame −2. We thus developed a method based on careful evolutionary analysis of the presence/absence of stop codons, revealing that ASP does impose significant selection pressure. All of these results support the idea that asp is the 10th gene of HIV-1 group M and indicate a correlation with the spread of the pandemic.HIV-1 | asp and env genes | overlapping genes | phylogenetic analyses | selection pressure

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“…If the provirus integrates in introns of host genes, the HIV antisense transcripts are spliced out and rapidly degraded. Nevertheless, HIV antisense transcripts have been detected (39,40), and they could provide an estimate of transcriptional interference in latently infected cells.…”

Section: Historical Perspectivementioning

confidence: 99%

Molecular mechanisms of HIV latency

Cary¹,

Fujinaga²,

Peterlin³

2016

Journal of Clinical Investigation

123

133

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Detection, characterization and regulation of antisense transcripts in HIV-1

Abstract: These results demonstrate for the first time that antisense transcription exists in HIV-1 in the context of infection. Possible translation of the predicted antisense ORF in this transcript should thus be re-examined.

Cited by 106 publications

References 42 publications

Immune Screening Identifies Novel T Cell Targets Encoded by Antisense Reading Frames of HIV-1

Immune Screening Identifies Novel T Cell Targets Encoded by Antisense Reading Frames of HIV-1

Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic

Molecular mechanisms of HIV latency

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