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![Location of the 5 CpGIs in the HIV-1 genome. The locations of the 5 CpGIs as described by Chavéz et al. [12] are indicated by red bars. CpGI long terminal repeat (LTR) and non-coding region (NCR) are located around the HIV-1 promoter location. CpGI ENV and env-tat-rev are located in the env gene. The fifth CpGI (3′ LTR) is located in the 3′ LTR region, where the antisense promoter region is found](publication/339589272/figure/fig1/AS:863891907178496@1582979289129/Location-of-the-5-CpGIs-in-the-HIV-1-genome-The-locations-of-the-5-CpGIs-as-described-by.png)
Location of the 5 CpGIs in the HIV-1 genome. The locations of the 5 CpGIs as described by Chavéz et al. [12] are indicated by red bars. CpGI long terminal repeat (LTR) and non-coding region (NCR) are located around the HIV-1 promoter location. CpGI ENV and env-tat-rev are located in the env gene. The fifth CpGI (3′ LTR) is located in the 3′ LTR region, where the antisense promoter region is found
Source publication
Background:
The HIV-1 proviral genome harbors multiple CpG islands (CpGIs), both in the promoter and intragenic regions. DNA methylation in the promoter region has been shown to be heavily involved in HIV-1 latency regulation in cultured cells. However, its exact role in proviral transcriptional regulation in infected individuals is poorly underst...
Contexts in source publication
Context 1
... HIV-1 genome encodes five CpGIs [12]: two are surrounding the promoter region and flanking the HIV-1 transcription start site and several transcription factor binding sites (e.g., TCF-1α, NF-κB, SP1) at the 5′ long terminal repeat (LTR) region (CpGI LTR in the U3 region of the 5′ LTR and CpGI non-coding region (NCR), downstream the HIV-1 5′ LTR (Fig. 1)) [12]. Two other CpGIs are located in the env gene (CpGI ENV (35% conserved) and CpGI env-tat-rev (ETR)), surrounding the HIV-1 antisense open reading frame (Fig. 1) [12,31]. The fifth CpGI is located in the 3′ LTR, where the antisense transcription start site is located [12,31]. In cultured HIV-1-infected cells, the regulatory role of ...
Context 2
... sites (e.g., TCF-1α, NF-κB, SP1) at the 5′ long terminal repeat (LTR) region (CpGI LTR in the U3 region of the 5′ LTR and CpGI non-coding region (NCR), downstream the HIV-1 5′ LTR (Fig. 1)) [12]. Two other CpGIs are located in the env gene (CpGI ENV (35% conserved) and CpGI env-tat-rev (ETR)), surrounding the HIV-1 antisense open reading frame (Fig. 1) [12,31]. The fifth CpGI is located in the 3′ LTR, where the antisense transcription start site is located [12,31]. In cultured HIV-1-infected cells, the regulatory role of proviral promoter methylation in viral transcriptional activity is clearly demonstrated: hypermethylation stabilizes HIV-1 latency and demethylating agents can ...
Context 3
... HIV-1-positive PBMC samples from that study were selected. Patients were divided into four cohorts based on their disease status (Additional Figure 1). The detailed study design and inclusion criteria have been described previously [39]. ...
Context 4
... of DNA methylation in the promoter region, even in patients suppressing VL successfully, therefore not following the predictions from the in vitro experiments [37,38]. It has been shown that DNA methylation behavior in cell lines is often drastically different from that of in vivo cells due to completely different epigenetic environments and Fig. 3 HIV-1 proviral DNA methylation comparison between patient cohorts. a Summary of the methylation data in the LTR region (CpGI LTR + CpGI NCR) using average methylation over all CpGs in the region. b Summary of the methylation data in the env region (CpGI ENV + CpGI ETR) using average methylation over all CpGs in the region. q = FDR-corrected ...
Citations
... Epigenetic modification of HIV-1 chromatin (e.g., methylation/demethylation) alters its structure to activate or repress transcription [21][22][23]. While repressive histone marks are found at the latent HIV-1 LTR, widespread and stable DNA methylation is lacking [24][25][26][27][28][29][30]. ...
Despite remarkable progress, a cure for HIV‑1 infection remains elusive. Rebound competent latent and transcriptionally active reservoir cells persevere despite antiretroviral therapy and rekindle infection due to inefficient proviral silencing. We propose a novel “block-lock-stop” approach, entailing long term durable silencing of viral expression towards an irreversible transcriptionally inactive latent provirus to achieve long term antiretroviral free control of the virus. A graded transformation of remnant HIV‑1 in PLWH from persistent into silent to permanently defective proviruses is proposed, emulating and accelerating the natural path that human endogenous retroviruses (HERVs) take over millions of years. This hypothesis was based on research into delineating the mechanisms of HIV‑1 latency, lessons from latency reversing agents and advances of Tat inhibitors, as well as expertise in the biology of HERVs. Insights from elite controllers and the availability of advanced genome engineering technologies for the direct excision of remnant virus set the stage for a rapid path to an HIV‑1 cure.
... Such interactions have also been described for cis-acting elements involved in regulating the alternative splicing of HIV-1 transcripts [91]. In addition, sequences within the HIV-1 env gene have been identified as potential elements that control intragenic transcriptional activity and include transcription binding sites, the presence of methylated CpG islands, and increased DNAse I sensitivity which correlates with transcriptionally active elements [92][93][94]. We have extended these observations using 5ʹ RACE PCR to demonstrate that HIV transcripts are generated from an intragenic promoter within the envelope gene in in vitro infected primary cells [95]. ...
Defective HIV-1 proviruses represent a population of viral genomes that are selected for by immune pressures, and clonally expanded to dominate the persistent HIV-1 proviral genome landscape. There are examples of RNA and protein expression from these compromised genomes which are generated by a variety of mechanisms. Despite the evidence that these proviruses are transcribed and translated, their role in HIV pathogenesis has not been fully explored. The potential for these genomes to participate in immune stimulation is particularly relevant considering the accumulation of cells harboring these defective proviruses over the course of antiretroviral therapy in people living with HIV. The expression of defective proviruses in different cells and tissues could drive innate sensing mechanisms and inflammation. They may also alter antiviral T cell responses and myeloid cell functions that directly contribute to HIV-1 associated chronic comorbidities. Understanding the impact of these defective proviruses needs to be considered as we advance cure strategies that focus on targeting the diverse population of HIV-1 proviral genomes.
Graphical abstract
... DNAm of host genes in response to HIV-1 infection has been implicated in mechanisms of viral latency, HIV-1 transcription, and viral replication [17][18][19]. As an example, HIV-1 can trigger methylation of host genes directly by inducing the DNA methyl transferase-1 enzyme in vitro [20]. ...
Despite significant advances in the treatment and care of people with HIV (PWH), several challenges remain in our understanding of disease pathogenesis to improve patient care. HIV infection can modify the host epigenome and as such can impact disease progression, as well as the molecular processes driving non-AIDS comorbidities in PWH. Epigenetic epidemiologic studies including epigenome-wide association studies (EWAS) offer a unique set of tools to expand our understanding of HIV disease and to identify novel strategies applicable to treatment and diagnosis in this patient population. In this review, we summarize the current state of knowledge from epigenetic epidemiologic studies of PWH, identify the main challenges of this approach, and highlight future directions for the field. Emerging epigenetic epidemiologic studies of PWH can expand our understanding of HIV infection and health outcomes, improve scientific validity through collaboration and replication, and increase the coverage of diverse populations affected by the global HIV pandemic. Through this review, we hope to highlight the potential of EWAS as a tool for HIV research and to engage more investigators to explore its application to important research questions.
... In host cells, DNA methylation of provirus promoter regions have been shown to regulate HIV-1 latency and transcription activation (119). In addition, RNA methylation has recently been recognized as an important factor in HIV-1 RNA metabolism and replication (120). ...
The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral life cycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in Next-Generation Sequencing (NGS) technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.
... Several epigenetic changes, particularly DNA methylation of genes, have been described in HIV transcriptional silencing and have been explored as targets for HIV-1 latency reversal strategies [19]. DNA methylation is a synthetic, reversible, and heritable epigenetic mark, and DNA methylation of CpG dense zones at gene promoters is often associated with direct or indirect transcriptional repression, termed CpG islands [20]. ...
Background
Therapeutic studies against human immunodeficiency virus type 1 (HIV-1) infection have become one of the important works in global public health.
Methods
Differential expression analysis was performed between HIV-positive (HIV+) and HIV-negative (HIV-) patients for GPL6947 and GPL10558 of GSE29429. Coexpression analysis of common genes with the same direction of differential expression identified modules. Module genes were subjected to enrichment analysis, Short Time-series Expression Miner (STEM) analysis, and PPI network analysis. The top 100 most connected genes in the PPI network were screened to construct the LASSO model, and AUC values were calculated to identify the key genes. Methylation modification of key genes were identified by the chAMP package. Differences in immune cell infiltration between HIV + and HIV- patients, as well as between antiretroviral therapy (ART) and HIV + patients, were calculated using ssGSEA.
Results
We obtained 3610 common genes, clustered into nine coexpression modules. Module genes were significantly enriched in interferon signalling, helper T-cell immunity, and HIF-1-signalling pathways. We screened out module genes with gradual changes in expression with increasing time from HIV enrolment using STEM software. We identified 12 significant genes through LASSO regression analysis, especially proteasome 20S subunit beta 8 (PSMB8) and interferon alpha inducible protein 27 (IFI27). The expression of PSMB8 and IFI27 were then detected by quantitative real-time PCR. Interestingly, IFI27 was also a persistently dysregulated gene identified by STEM. In addition, 10 of the key genes were identified to be modified by methylation. The significantly infiltrated immune cells in HIV + patients were restored after ART, and IFI27 was significantly associated with immune cells.
Conclusion
The above results provided potential target genes for early diagnosis and treatment of HIV + patients. IFI27 may be associated with the progression of HIV infection and may be a powerful target for immunotherapy.
... The existence of intragenic promoters has been suggested for several retroviruses [45][46][47][48][49]. The presence of proviral cis-regulatory elements has also been proposed within the HIV-1 genome, with reports of DNAse hypersensitive sites, methylated CpG islands, transcription factor DNA binding sites and modest transcriptional activation potential [27,31,32,50,51]. However, the regulatory mechanisms which control transcription of alternative transcriptional start sites in HIV remain largely undescribed. ...
... Taken together, our data generated from yeast-one-hybrid transcription factor binding assays, promoter prediction software, transfections with deletion and reporter plasmids, and 5' RACE sequencing, indicate cis-transcriptional elements and promoters located at approximately +7,800 bp in the HIV-1 proviral genome. This observed transcriptional activity overlaps with previously reported CpG islands [51]. The transcripts generated originate in the env gene, span the tat splice junction, and include intronic sequence. ...
HIV-1 establishes a persistent proviral reservoir by integrating into the genome of infected host cells. Current antiretroviral treatments do not target this persistent population of proviruses which include latently infected cells that upon treatment interruption can be reactivated to contribute to HIV-1 rebound. Deep sequencing of persistent HIV proviruses has revealed that greater than 90% of integrated HIV genomes are defective and unable to produce infectious virions. We hypothesized that intragenic elements in the HIV genome support transcription of aberrant HIV-1 RNAs from defective proviruses that lack long terminal repeats (LTRs). Using an intact provirus detection assay, we observed that resting CD4+ T cells and monocyte-derived macrophages (MDMs) are biased towards generating defective HIV-1 proviruses. Multiplex reverse transcription droplet digital PCR identified env and nef transcripts which lacked 5’ untranslated regions (UTR) in acutely infected CD4+ T cells and MDMs indicating transcripts are generated that do not utilize the promoter within the LTR. 5’UTR-deficient env transcripts were also identified in a cohort of people living with HIV (PLWH) on ART, suggesting that these aberrant RNAs are produced in vivo . Using 5’ rapid amplification of cDNA ends (RACE), we mapped the start site of these transcripts within the Env gene. This region bound several cellular transcription factors and functioned as a transcriptional regulatory element that could support transcription and translation of downstream HIV-1 RNAs. These studies provide mechanistic insights into how defective HIV-1 proviruses are persistently expressed to potentially drive inflammation in PLWH.
... A recent study examined methylation of intragenic regions of the proviral genome across four groups of HIV infected individuals [i.e. long term non-progressors, early combination ART (cART) treated, late cART treated and cART naïve, acutely infected] (74). As a whole, methylation of promoter regions was reduced in all four groups, while high levels of methylation were observed in the intragenic env region. ...
... As a whole, methylation of promoter regions was reduced in all four groups, while high levels of methylation were observed in the intragenic env region. In the ART naïve acutely infected group, a distinct increase in 5'LTR and a decrease in intragenic env methylation was observed (74). Taken together, these observations suggest that intragenic methylation could be a late event during infection as well as intragenic methylation was positively associated with CD4+ counts and viral loads (74). ...
... In the ART naïve acutely infected group, a distinct increase in 5'LTR and a decrease in intragenic env methylation was observed (74). Taken together, these observations suggest that intragenic methylation could be a late event during infection as well as intragenic methylation was positively associated with CD4+ counts and viral loads (74). ...
With approximately 38 million people living with HIV/AIDS globally, and a further 1.5 million new global infections per year, it is imperative that we advance our understanding of all factors contributing to HIV infection. While most studies have focused on the influence of host genetic factors on HIV pathogenesis, epigenetic factors are gaining attention. Epigenetics involves alterations in gene expression without altering the DNA sequence. DNA methylation is a critical epigenetic mechanism that influences both viral and host factors. This review has five focal points, which examines (i) fluctuations in the expression of methylation modifying factors upon HIV infection (ii) the effect of DNA methylation on HIV viral genes and (iii) host genome (iv) inferences from other infectious and non-communicable diseases, we provide a list of HIV-associated host genes that are regulated by methylation in other disease models (v) the potential of DNA methylation as an epi-therapeutic strategy and biomarker. DNA methylation has also been shown to serve as a robust therapeutic strategy and precision medicine biomarker against diseases such as cancer and autoimmune conditions. Despite new drugs being discovered for HIV, drug resistance is a problem in high disease burden settings such as Sub-Saharan Africa. Furthermore, genetic therapies that are under investigation are irreversible and may have off target effects. Alternative therapies that are nongenetic are essential. In this review, we discuss the potential role of DNA methylation as a novel therapeutic intervention against HIV.
... Due to the specificity of ZFP362, we have not tested its potency on other HIV-1 subtypes, although ZFP362 fused to an activator domain has been found to activate clades A-E of HIV-1 15 . Another limitation, rooted in the observation that HIV-1 LTR DNA hypermethylation is not found to be significantly enriched in latent reservoirs from long-term nonprogressors of AIDS 53,54 , corroborates the findings reported herein that significant DNA methylation does not lead to a consistent reduction of viral load in the mice models. ...
Human Immunodeficiency Virus (HIV-1) produces a persistent latent infection. Control of HIV-1 using combination antiretroviral therapy (cART) comes at the cost of life-shortening side effects and development of drug-resistant HIV-1. An ideal and safer therapy should be deliverable in vivo and target the stable epigenetic repression of the virus, inducing a stable “block and lock” of virus expression. Towards this goal, we developed an HIV-1 promoter-targeting Zinc Finger Protein (ZFP-362) fused to active domains of DNA methyltransferase 3 A to induce long-term stable epigenetic repression of HIV-1. Cells were engineered to produce exosomes packaged with RNAs encoding this HIV-1 repressor protein. We find here that the repressor loaded anti-HIV-1 exosomes suppress virus expression and that this suppression is mechanistically driven by DNA methylation of HIV-1 in humanized NSG mouse models. The observations presented here pave the way for an exosome-mediated systemic delivery platform of therapeutic cargo to epigenetically repress HIV-1 infection. A strategy to control HIV-1 infection is to stably repress HIV-1 and induce “deep latency”. Here the authors show that a recombinant anti-HIV-1-1 protein can be packaged as mRNA into exosomes and delivered systemically to repress HIV-1-1 within the context of virus infected mice and achieve long term silencing of HIV-1-1 expression.
... Some studies found that Forkhead box-P3 (FOXP3, a master TF for regulating differentiation and suppressive functions of Treg cells) expression increased in AIDS patients and repressed HIV-1 transcription [120,121]. Previous studies [120,122] discovered that DNA methylation was altered during HIV-1 infection. Demethylation of the FOXP3 promoter was significantly higher in AIDS patients than in healthy ones, which led to the high FOXP3 expression and increased number of Treg cells in the gut mucosa. ...
AIDS first emerged decades ago; however, its cure, i.e., eliminating all virus sources, is still unachievable. A critical burden of AIDS therapy is the evasive nature of HIV-1 in face of host immune responses, the so-called “latency.” Recently, a promising approach, the “Shock and Kill” strategy, was proposed to eliminate latently HIV-1-infected cell reservoirs. The “Shock and Kill” concept involves two crucial steps: HIV-1 reactivation from its latency stage using a latency-reversing agent (LRA) followed by host immune responses to destroy HIV-1-infected cells in combination with reinforced antiretroviral therapy to kill the progeny virus. Hence, a key challenge is to search for optimal LRAs. Looking at epigenetics of HIV-1 infection, researchers proved that some bromodomains and extra-terminal motif protein inhibitors (BETis) are able to reactivate HIV-1 from latency. However, to date, only a few BETis have shown HIV-1-reactivating functions, and none of them have yet been approved for clinical trial. In this review, we aim to demonstrate the epigenetic roles of BETis in HIV-1 infection and HIV-1-related immune responses. Possible future applications of BETis and their HIV-1-reactivating properties are summarized and discussed.
... In recent years, some studies have found that the role of intragenic methylation is seriously underestimated. In fact, intragenic and promoter methylations are both involved in transcriptional regulation of HIV-1 and reduce transcription efficiency of the virus [55]. Ma et al. found that putative promoters may exist in the gene bodies of certain cancer-related genes. ...
Background
Diabetic osteoporosis (DOP) is a systemic metabolic bone disease caused by diabetes mellitus (DM). Adipose-derived stem cells (ASCs) play an important role in bone regeneration. Our previous study confirmed that ASCs from DOP mice (DOP-ASCs) have a lower osteogenesis potential compared with control ASCs (CON-ASCs). However, the cause of this poor osteogenesis has not been elucidated. Therefore, this study investigated the underlying mechanism of the decline in the osteogenic potential of DOP-ASCs from the perspective of epigenetics and explored methods to enhance their osteogenic capacity.
Methods
The expression level of JNK1-associated membrane protein (JKAMP) and degree of DNA methylation in CON-ASCs and DOP-ASCs were measured by mRNA expression profiling and MeDIP sequencing, respectively. JKAMP small interfering RNA (siRNA) and a Jkamp overexpression plasmid were used to assess the role of JKAMP in osteogenic differentiation of CON-ASCs and DOP-ASCs. Immunofluorescence, qPCR, and western blotting were used to measure changes in expression of Wnt signaling pathway-related genes and osteogenesis-related molecules after osteogenesis induction. Alizarin red and ALP staining was used to confirm the osteogenic potential of stem cells. Bisulfite-specific PCR (BSP) was used to detect JKAMP methylation degree.
Results
Expression of JKAMP and osteogenesis-related molecules (RUNX2 and OPN) in DOP-ASCs was decreased significantly in comparison with CON-ASCs. JKAMP silencing inhibited the Wnt signaling pathway and reduced the osteogenic ability of CON-ASCs. Overexpression of JKAMP in DOP-ASCs rescued the impaired osteogenic capacity caused by DOP. Moreover, JKAMP in DOP-ASCs contained intragenic DNA hypermethylated regions related to the downregulation of JKAMP expression.
Conclusions
Intragenic DNA methylation inhibits the osteogenic ability of DOP-ASCs by suppressing expression of JKAMP and the Wnt signaling pathway. This study shows an epigenetic explanation for the reduced osteogenic ability of DOP-ASCs and provides a potential therapeutic target to prevent and treat osteoporosis.
