Next Article in Journal
Microtubule Retrograde Motors and Their Role in Retroviral Transport
Next Article in Special Issue
Differences in HIV Markers between Infected Individuals Treated with Different ART Regimens: Implications for the Persistence of Viral Reservoirs
Previous Article in Journal
Fc-Based Recombinant Henipavirus Vaccines Elicit Broad Neutralizing Antibody Responses in Mice
Previous Article in Special Issue
Toward Structurally Novel and Metabolically Stable HIV-1 Capsid-Targeting Small Molecules
Open AccessArticle

Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci

1
Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato-SS554, 09042 Monserrato, Cagliari, Italy
2
Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Cagliari, Italy
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(4), 481; https://doi.org/10.3390/v12040481
Received: 9 March 2020 / Revised: 20 April 2020 / Accepted: 20 April 2020 / Published: 23 April 2020
(This article belongs to the Special Issue Antiretroviral Drug Development and HIV Cure Research)
Human endogenous retrovirus (HERV) expression is currently studied for its possible activation by HIV infection. In this context, the HERV-K(HML2) group is the most investigated: it has been proposed that HIV-1 infection can prompt HML2 transcription, and that HML2 proteins can affect HIV-1 replication, either complementing HIV or possibly influencing antiretroviral therapy. However, little information is available on the expression of other HERV groups in HIV infection. In the present study, we used a bioinformatics pipeline to investigate the transcriptional modulation of approximately 3250 well-characterized HERV loci, comparing their expression in a public RNA-seq profile, including a HIV-1-infected and a control T cell culture. In our pilot study, we found approximately 200 HERV loci belonging to 35 HERV groups that were expressed in one or both conditions, with transcripts per million (TPM) values from 1 to >500. Intriguingly, HML2 elements constituted only the 3% of expressed HERV loci, and in most cases (160) HERV expression was downregulated in the HIV-infected culture, showing from a 1- to 14-fold decrease as compared to uninfected cells. HERV transcriptome has been inferred de novo and employed to predict a total of about 950 HERV open reading frames (ORFs). These have been validated according to the coding potential and estimated abundance of the corresponding transcripts, leading to a set of 57 putative proteins potentially encoded by 23 HERV loci. Analysis showed that some individual loci have a coding potential that deserves further investigation. Among them, a HML6 provirus at locus 19q13.43 was predicted to produce a transcript showing the highest TPM among HERV-derived transcripts, being upregulated in HIV+ cells and inferred to produce Gag and Env puteins with possible biological activity. View Full-Text
Keywords: HERV; HIV; endogenous retroviruses; RNAseq; HERV expression; HML2 HERV; HIV; endogenous retroviruses; RNAseq; HERV expression; HML2
Show Figures

Graphical abstract

MDPI and ACS Style

Grandi, N.; Pisano, M.P.; Scognamiglio, S.; Pessiu, E.; Tramontano, E. Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci. Viruses 2020, 12, 481.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop