Biology subjects

Dionellis, V. S.

Publications and source records attributed to Dionellis, V. S..

3 recordsLinked to original sources

bioRxiv2025

Human POLD3 coordinates leading and lagging strand in Mitotic DNA Synthesis

Deregulation of origin firing and licensing, shortage of deoxyribonucleotides in the cell and interference between transcription and replication are among the causes of DNA replication stress in cancer cells. This leads in various ways (notably, through common fragile sites expression and incomplete replication of late-replicating genomic regions during S phase) to the necessity of finishing DNA replication in mitosis by a mechanism called Mitotic DNA synthesis (MiDAS), which is related to Break-Induced Replication (BIR). Even if it is of primary importance for cancer cells, the molecular mechanism of MiDAS, and generally of BIR, is not yet well understood. Recently, the third subunit of the eukaryotic DNA polymerase delta (POLD3) has been recognized as a key player of BIR, though its role is not yet clear. In this work, using a protocol established in our group to map at high resolution newly replicated DNA at MiDAS sites, we provide new insights into the molecular role of POLD3 in this repair mechanism. In particular, by analyzing MiDAS in mutant HeLa clones lacking the PCNA-interacting domain of POLD3, we demonstrate that the interaction between POLD3 and PCNA is required for coordinating leading and lagging strand synthesis in MiDAS. This work represents an important step forward towards the comprehension of the molecular mechanisms of Mitotic DNA synthesis, the full understanding of which is of primary importance for the possible development of novel cancer therapies targeting BIR-related pathways.

molecular biology↗

bioRxiv2025

Pluripotency factors enhance the firing efficiency of late DNA replication origins in mouse embryonic stem cells

DNA replication initiates at genomic loci known as origins, which fire according to a spatiotemporal program, still not yet well-defined in mammals. Here, we investigated whether pluripotent mouse embryonic stem cells (mESCs), which proliferate rapidly and have very short G1 phases, have a different spatiotemporal origin firing program than differentiated cells. Using EdU-seq combined with various cell cycle synchronization methods, we identified DNA replication initiation zones (IZs) in mESCs, mesenchymal stem cells and mouse embryo fibroblasts (MEFs). Similar profiles of IZs were present in the early-replicating genomic domains in all cell types. Uniquely in mESCs, we observed, within 1-2 hours of entry into S phase, origin firing at IZs that mapped to the mid and late-replicating genomic domains. This change in the replication timing program, which did not lead to shortening of the length of S phase, was driven by pluripotency transcription factors, notably OCT4, as documented by examining mESCs in which OCT4 expression was transiently suppressed. We propose that pluripotency factors in mESCs bind to IZs at mid and late-replicating genomic domains to enhance chromatin accessibility, which in turn leads to changes in the replication timing program. These results provide an example of how transcription factors control DNA replication in a cell type-specific manner.

molecular biology↗

bioRxiv2020

Identification of low micromolar SARS-CoV-2 Mpro inhibitors from hits identified by in silico screens

Mpro, also known as 3CLpro, is the main protease of the SARS-CoV-2 coronavirus and, as such, is essential for the viral life cycle. Two studies have each screened and ranked in silico more than one billion chemical compounds in an effort to identify putative inhibitors of Mpro. More than five hundred of the seven thousand top-ranking hits were synthesized by an external supplier and examined with respect to their activity in two biochemical assays: a protease activity assay and a thermal shift assay. Two clusters of chemical compounds with Mpro inhibitory activity were identified. An additional five hundred molecules, analogues of the compounds in the two clusters described above, were also synthesized and characterized in vitro. The study of the analogues revealed that the compounds of the first cluster acted by denaturing Mpro and might denature other proteins as well. In contrast, the compounds of the second cluster targeted Mpro with much greater specificity and enhanced its melting temperature, consistent with the formation of stable Mpro-inhibitor complexes. The most active compounds of the second cluster exhibited IC50 values between 4 and 7 M and their chemical structure suggests that they could serve as leads for the development of potent Mpro inhibitors.

biochemistry↗