Biology subjects

Arif, R.

Publications and source records attributed to Arif, R..

4 recordsLinked to original sources

bioRxiv2026

The HIV-1 restriction factor RPRD2 does not inhibit transcription of HIV-1 or endogenous retroelements

A vital question in transcription regulation is how and to what extent transcription of different DNA species, including viral DNA, episomal DNA and endogenous retroelements, is differentially regulated to transcription of host genes. RPRD2 has previously been characterized as an HIV restriction factor that blocks reverse transcription. However, RPRD2 has also been characterized as a regulator of global transcription of host genes. Therefore, we hypothesized that RPRD2 may also regulate nascent transcription from HIV provirus and endogenous retroelements. First, we used a combination of experimental and computational methods to characterize the binding of RPRD2 to RNA and DNA:RNA hybrids. Using immunoprecipitation, we identified that RPRD2 interacts with both the transcription regulator PAF1 and the HUSH complex member TASOR, independently. Immunofluorescence revealed that GFP-RPRD2 localizes to foci in the nucleus, and these foci overlap with nuclear speckles. To measure the effect of RPRD2 on transcription, we used plasmid-borne HIV LTR-driven reporter constructs and observed that RPRD2 depletion increased transcription of constructs both with and without an intron. We next investigated transcription from integrated proviruses and found no effect of RPRD2 depletion using several different systems. Lastly, we measured transcription of endogenous retroelements and found that RPRD2 depletion did not affect transcription of LINE-1 or HERV-K. Finally, we investigated whether RPRD2 regulates production of IFN in response to nucleic acid species or affects transcription of IFN-stimulated genes. We found that depletion of RPRD2 had no effect on IFN production or ISG expression. Together, our findings demonstrate how regulation of transcription is not universal for host genes, integrated provirus, unintegrated plasmid and endogenous retroviruses, and confirmed that although RPRD2 governs cellular transcription, it does not regulate transcription of HIV-1 provirus or of endogenous retroelements.

microbiology↗

bioRxiv2026

Transcriptional regulation of the TASK-1 potassium channel by ETV1 -Implications for atrial excitability

BackgroundAtrial fibrillation (AF), the most common sustained arrhythmia, is driven by electrical and structural remodelling, including altered ion channel expression. The atrial-specific potassium channel TASK-1 regulates action potential duration (APD) and is differentially expressed in AF and left ventricular dysfunction, but the mechanisms controlling its expression are not well understood. ObjectiveThis study examines whether the transcription factor ETV1 regulates TASK-1 and contributes to atrial electrical remodelling. MethodsAtrial tissue from patients with and without AF was analysed to assess the relationship between ETV1 and TASK-1 (KCNK3) expression. In HL-1 cardiomyocyte-like cells and native fibroblasts, ETV1 activity was reduced using pharmacological inhibition or siRNA-mediated knockdown. TASK-1 expression, TASK-1 current, and APD at 90% repolarization were measured. Pacing experiments tested activity-dependent TASK-1 regulation. Direct transcriptional regulation was evaluated using ChIP-qPCR and ChIP-seq to detect ETV1 binding at the KCNK3 promoter. ResultsETV1 and TASK-1 levels were positively correlated in human atrial tissue. In HL-1 cells and fibroblasts, ETV1 inhibition or knockdown decreased TASK-1 expression and current and selectively prolonged APD90. Pacing-induced upregulation of TASK-1 was prevented by ETV1 inhibition, indicating a protective effect against pro-arrhythmic remodelling. ChIP-qPCR and ChIP-seq confirmed direct ETV1 binding to the KCNK3 promoter. ConclusionETV1 directly regulates TASK-1 expression and contributes to atrial electrical remodelling, identifying ETV1 as a potential upstream therapeutic target in AF. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/711402v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@3e5b25org.highwire.dtl.DTLVardef@1d1f909org.highwire.dtl.DTLVardef@34cf37org.highwire.dtl.DTLVardef@1105539_HPS_FORMAT_FIGEXP M_FIG C_FIG Translational perspectiveAtrial fibrillation is sustained by maladaptive electrical remodelling that remains insufficiently addressed by current rhythm-control therapies. Direct inhibition of individual ion channels has shown efficacy but is limited by phenotype dependence and proarrhythmic risk. The present data identify ETV1 as an upstream transcriptional regulator of the atrial-specific potassium channel TASK-1. Modulation of ETV1 reduced TASK-1 expression, prolonged atrial repolarisation, and prevented tachycardia-induced electrical remodelling in vitro. Targeting ETV1 may therefore represent a disease-modifying strategy that intervenes earlier in the remodelling cascade than conventional antiarrhythmic drugs. This approach could enable phenotype-guided therapy in atrial cardiomyopathy, particularly in patients with preserved ventricular function, and warrants validation in translational large-animal and clinical studies.

molecular biology↗

bioRxiv2025

SFTSV NSs protein is a novel tick antiviral RNAi response suppressor

Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne phenuivirus causing high mortality in humans. While the non-structural protein NSs is dispensable for replication in interferon-deficient mammalian cells, we demonstrate for the first time that NSs is essential for viral replication in tick cells. SFTSV infection triggers canonical Dicer-2-mediated antiviral RNA interference (RNAi) in tick cells, producing virus-derived small interfering RNAs (siRNAs) that target viral transcripts for degradation. We show that NSs functions as a viral suppressor of RNAi by selectively engaging and depleting single-stranded RNAs derived from 22-nucleotide siRNAs, likely limiting their incorporation into RNA-induced silencing complexes (RISC). Complementation with a heterologous RNAi suppressor (p19 protein) partially rescues replication of NSs-deficient virus, validating the RNAi suppressive function of NSs. These findings reveal that successful tick-borne viral replication requires host-specific immune evasion strategies and establish NSs-mediated RNAi suppression as essential for SFTSV persistence in arthropod vectors. Significance StatementThis study reveals a critical requirement for SFTSV infection that differs between hosts. While the viral NSs protein is dispensable in interferon deficient mammalian cells, it is essential for replication in tick cells, the natural vectors of the virus. We show that NSs functions as a viral RNA silencing suppressor by associating with virus derived small RNAs and limiting their availability to the tick antiviral RNA interference machinery. This provides mechanistic insight into how tick-borne viruses evade arthropod immune defences through engagement of functional siRNAs rather than broad inhibition of RNA interference pathways. Together, these findings demonstrate that SFTSV employs distinct immune evasion strategies in different hosts and identify NSs as a key determinant of vector cell infection.

microbiology↗

bioRxiv2024

The PAZ domain of Aedes aegypti Dicer 2 is critical for accurate and high-fidelity size determination of virus-derived small interfering RNAs.

The exogenous siRNA (exo-siRNA) pathway is a critical RNA interference response involved in controlling arbovirus replication in mosquito cells. It is initiated by the detection of viral long double-stranded RNA (dsRNA) by the RNase III enzyme Dicer 2 (Dcr2), which is processed into predominantly 21 nucleotide (nt) virus-derived small interfering RNAs, or vsiRNAs that are taken up by the Argonaute 2 (Ago2) protein to target viral single-stranded RNAs. The detailed understanding of Dicer structure, function and domains owes much to studies outside the context of viral infection, and how Dcr2 domains contribute to detecting viral dsRNA to mount antiviral responses in infected mosquito cells remains much less understood. Here, we used a Dcr2 reconstitution system in Aedes aegypti derived Dcr2 KO cells to assess the contribution of the PAZ domain to induction of the exo-siRNA pathway following infection with Semliki Forest virus (SFV; Togaviridae, Alphavirus). Amino acids critical for PAZ activity were identified, and loss of PAZ function affected the production of 21 nt vsiRNAs -though not the overall ability of Dcr2 to process viral dsRNA- and silencing activity. This study establishes the importance of correct vsiRNA size in mosquito exo-siRNA antiviral responses, as well as the PAZ domains functional contribution to Dcr2 processing of viral dsRNA to 21 nt vsiRNAs.

microbiology↗