Underestimated effect of intragenic HIV-1 DNA methylation on viral transcription in infected individuals

Kint, Sam; Trypsteen, Wim; Spiegelaere, Ward De; Malatinková, Eva; Loés, Sabine Kinloch-de; Meyer, Tim De; Criekinge, Wim Van; Vandekerckhove, Linos

doi:10.1186/s13148-020-00829-1

Cited by 15 publications

(16 citation statements)

References 61 publications

(109 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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(50). The transcripts generated originate in the Env gene, span the Tat splice junction, and include intronic sequence.…”

Section: Discussionsupporting

confidence: 91%

Intragenic proviral elements support transcription of defective HIV-1 proviruses

Armstrong

Bernabe

Berenson

et al. 2021

Preprint

View full text Add to dashboard Cite

HIV 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 digital drop 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.

show abstract

Section: Discussionsupporting

confidence: 91%

Intragenic proviral elements support transcription of defective HIV-1 proviruses

Armstrong

Bernabe

Berenson

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…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.…”

Section: Discussionsupporting

confidence: 77%

Exosome-mediated stable epigenetic repression of HIV-1

et al. 2021

View full text Add to dashboard Cite

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.

show abstract

“…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.…”

Section: Discussionmentioning

confidence: 99%

JKAMP inhibits the osteogenic capacity of adipose-derived stem cells in diabetic osteoporosis by modulating the Wnt signaling pathway through intragenic DNA methylation

et al. 2021

View full text Add to dashboard Cite

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.

show abstract

Underestimated effect of intragenic HIV-1 DNA methylation on viral transcription in infected individuals

Cited by 15 publications

References 61 publications

Intragenic proviral elements support transcription of defective HIV-1 proviruses

Intragenic proviral elements support transcription of defective HIV-1 proviruses

Exosome-mediated stable epigenetic repression of HIV-1

JKAMP inhibits the osteogenic capacity of adipose-derived stem cells in diabetic osteoporosis by modulating the Wnt signaling pathway through intragenic DNA methylation

Contact Info

Product

Resources

About