Biology subjects

Jackson-Jones, K. A.

Publications and source records attributed to Jackson-Jones, K. A..

3 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↗

bioRxiv2025

Impact of N6-methyladenosine (m6A) machinery on HIV-1 replication in primary CD4+ T cells

N6-methyladenosine (m6A) is the most prevalent internal modification of cellular and viral RNA and is critical to the regulation of its localization, stability, and translation. Previous studies on the role of m6A during HIV-1 replication have produced conflicting results. Since m6A function can vary dramatically by cell type and state, here we aimed to clarify the role of the m6A machinery during HIV-1 replication in primary CD4+ T cells. Using CRISPR-Cas9 we targeted 46 cellular genes implicated in m6A or 5-methylcytosine (m5C) regulation and measured subsequent HIV-1 replication in primary CD4+ T cells. Only knockout of the m6A writer complex auxiliary proteins VIRMA and WTAP, and the m6A reader YTHDF2 were validated as significantly decreasing HIV-1 replication. In contrast, knockout of METTL3 or METTL14, which form the catalytic core of the writer complex, resulted in only marginal changes in HIV-1 infection, despite significant decreases in total cellular m6A levels. Chemical inhibition of METTL3 led to a dose-dependent decrease in HIV-1 infection, coupled with an increase in protein levels of METTL3 and other writer complex members. Expression of writer proteins was also co-dependent, revealing complex regulatory feedback mechanisms. Overall, these results clarify the role of epitranscriptomic machinery during HIV-1 replication in primary CD4+ T cells and suggest regulation by auxiliary members of the m6A writer complex is more influential than the function of the catalytic core itself on HIV-1 infection in primary CD4+ T cells. IMPORTANCEm6A is the most common chemical modification on cellular and viral RNA and regulates its stability, localization, and translation. m6A modification and its regulation varies dramatically between cell types and cell states. In this study, we investigated the role of m6A factors during HIV-1 infection of physiologically relevant primary CD4+ T cells. Using CRISPR-Cas9 to knockout 46 cellular genes implicated in RNA modification, we found only the m6A writer complex auxiliary members WTAP and VIRMA, and the reader YTHDF2, significantly affected HIV-1 replication in these cells. In contrast, knockout of METTL3 or METTL14, which form the catalytic core of the writer complex, resulted in marginal changes in HIV-1 infection, despite larger reductions in total cellular m6A levels. Our findings suggest regulation by auxiliary members of the m6A writer complex is more influential than the function of the catalytic core itself on HIV-1 infection in primary CD4+ T cells.

microbiology↗

bioRxiv2020

Identification of a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the Endoplasmic Reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Here, we show that NBAS fulfils an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 co-regulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER protective function by ensuring quality control of ER-translated mRNAs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/954453v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@172e4a3org.highwire.dtl.DTLVardef@9769org.highwire.dtl.DTLVardef@d478c1org.highwire.dtl.DTLVardef@143e0f9_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LINBAS is an NMD factor that localizes to the membrane of the endoplasmic reticulum (ER) C_LIO_LINBAS has dual, independent, roles in Golgi-to-ER retrograde transport and in ER-NMD C_LIO_LINBAS recruits the core NMD factor UPF1 to the membrane of the ER C_LIO_LIThe ER-NMD pathway targets for degradation mRNAs that are translated at the ER C_LI

molecular biology↗