Biology subjects

Richter, S. N.

Publications and source records attributed to Richter, S. N..

4 recordsLinked to original sources

bioRxiv2025

HTLV-1 antisense transcription is promoted by increased SP1 binding at 3'-LTR G-Quadruplexes

The human T-cell lymphotropic virus type 1 (HTLV-1) is a highly oncogenic delta-retrovirus. It presents 5- and 3-long terminal repeats (LTR) that are enriched in putative G-quadruplex (G4)-forming sequences. G4s are non-canonical nucleic acid structures that regulate key biological processes in both human and viral genomes. We here investigated the presence and functional role of G4s within the HTLV-1 3-LTR, which governs the antisense transcription of the viral bZIP factor (HBZ), the main responsible for T-cell transformation. We identified seven highly conserved sequences that folded into two-layer G4s in both single- and double-stranded DNA in vitro. We demonstrated G4 folding in infected cells by chromatin immunoprecipitation and showed SP1 enrichment at the 3-LTR G4s. We showed that G4 stabilization with a ligand enhances antisense transcription by promoting recruitment of SP1. Our findings unveil a G4-mediated regulatory mechanism sustaining HTLV-1 antisense transcription and provide new insights into the complex interplay between the HTLV-1 genome and host cellular factors, contributing to our understanding of retroviral replication strategies to be exploited as new therapeutic targets.

microbiology↗

bioRxiv2023

Identification of druggable host dependency factors shared by multiple SARS-CoV-2 variants of concern

The high mutation rate of SARS-CoV-2 leads to emergence of several variants, some of which are resistant to vaccines and drugs targeting viral elements. Targeting host dependency factors - cell proteins required for viral replication - would help avoid resistance. However, whether different SARS-CoV-2 variants induce conserved cell responses and exploit the same core host factors is still unclear. We compared three variants of concern and observed that the host transcriptional response was conserved, differing only in kinetics and magnitude. By CRISPR screening we identified the host genes required for infection by each variant: most of the identified genes were shared by multiple variants, both in lung and colon cells. We validated our hits with small molecules and repurposed FDA-approved drugs. All drugs were highly effective against all tested variants, including delta and omicron, new variants that emerged during the study. Mechanistically, we identified ROS production as a pivotal step in early virus propagation. Antioxidant drugs, such as N-acetyl cysteine (NAC), were effective against all variants both in human lung cells, and in a humanised mouse model. Our study supports the use of available antioxidant drugs, such as NAC, as a general and effective anti-COVID-19 approach.

microbiology↗

bioRxiv2020

Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome

Cell identity is maintained by activation of cell-specific gene programs, regulated by epigenetic marks, transcription factors and chromatin organization1-3. DNA G-quadruplex (G4)-folded regions in cells were reported to be associated with either increased or decreased transcriptional activity4,5. By G4 ChIP-seq/RNA-seq analysis on liposarcoma cells we confirmed that G4s in promoters are invariably associated with high transcription levels in open chromatin. Comparing G4 presence, location and transcript levels in liposarcoma cells to available data on keratinocytes, we showed that the same promoter sequences of the same genes in the two cell lines had different G4-folding state: high transcript levels consistently associated with high G4-folding. Transcription factors AP-1 and SP1, whose binding sites were the most significantly represented in G4-folded sequences, coimmunoprecipitated with their G4-folded promoters. Thus G4s and their associated transcription factors cooperate to determine cell-specific transcriptional programs, making G4s strongly emerge as new epigenetic regulators of the transcription machinery.

genomics↗

bioRxiv2020

Transcription factor recruitment by parallel G-quadruplexes to promote transcription: the case of herpes simplex virus-1 ICP4

G-quadruplexes (G4s), four-stranded nucleic acid structures that adopt several distinctive conformations, are abundant at gene promoters and have been proposed as transcription regulatory elements. G4s form in the herpes simplex virus-1 (HSV-1) genome during its viral cycle. Here by cross-linking/pull-down assay we identified ICP4 as the protein that most interacts with viral G4s during infection. In vitro and in infected cells, ICP4 specifically and directly bound and unfolded parallel G4s, including those present in HSV-1 immediate early gene promoters, and consequently induced transcription. This mechanism was also exploited by ICP4 to promote its own transcription. By proximity ligation assay we visualized ICP4 interaction at the single G4 in cells. G4 ligands inhibited ICP4 binding to G4s. Our results indicate the existence of a well-defined G4-viral protein network that regulates the productive HSV-1 cycle. They also point to G4s as elements that recruit transcription factors to activate transcription in cells.

microbiology↗