Biology subjects

Gonzalez Prieto, R.

Publications and source records attributed to Gonzalez Prieto, R..

5 recordsLinked to original sources

bioRxiv2026

RNF25 Ubiquitin E3 activity Safeguards Genome Integrity by Modulating DNA Replication, Transcription and Translation.

The human genome encodes several hundreds of ubiquitin E3 enzymes, most of which have poorly understood biological roles. In search for novel ubiquitin E3 enzymes involved in DNA damage tolerance, we identified RNF25 as a candidate to have a role in DNA replication stress tolerance. Under stress conditions, RNF25 translocates to the nucleus in a cGAS-dependent manner, and loss of RNF25 ubiquitin E3 activity leads to the accumulation of replication-dependent ssDNA gaps. Combining functional assays with with mass-spectrometry based proteomics approaches such as TULIP2, iPOND-MS and TurboID, we found that, mechanistically, RNF25 promotes the stability of the replication fork at Transcription-Replication Conflicts by the ubiquitin-mediated clearance of RAD18, mono-ubiquitinated PCNA, H2B-K120ub and RECQL, among others. Lack of RNF25 ubiquitin E3 activity promotes the occurrence of Transcription-Replication Conflicts and destabilizes reversed replication forks, enabling re-priming and accumulation of ssDNA gaps behind the replication fork, ultimately compromising genome integrity. Overall, RNF25 regulates DNA replication, transcription and translation in an ubiquitin-based goldilocks.

molecular biology↗

bioRxiv2026

Decoding the Mechanism of Action of a Parasite TGFβAntagonist Inspires the Creation of Cell-type-specific TGFβ Modulators

Heligmosomoides polygyrus, a mouse parasite, modulates host immunity by secreting modular transforming growth factor-{beta} (TGF{beta}) mimics (TGMs). The agonist TGM1 interacts with TGFBR1, TGFBR2, and the co-receptor CD44 through domains D1/2, D3, and D4/5, respectively. In contrast, the antagonist TGM6, which lacks D1/2, but retains TGFBR2 binding through D3, targets different subsets of cells compared to TGM1. The TGM6 co-receptor is unknown. Using X-ray crystallography and binding studies, we show that TGM6 preferentially binds mouse TGFBR2 over human TGFBR2, and that this is essential for its antagonistic function. We identified low-density lipoprotein receptor-related protein 1 (LRP1) and betaglycan (TGFBR3) as co-receptors for TGM6. LRP1 enhances TGM6 efficacy and is vital for its specific antagonistic effects by promoting TGFBR2 degradation, while betaglycan counteracts TGM6 in a TGFBR2-dependent manner. The modular organization of TGMs enabled us to rationally design TGM1/6 chimeras or TGM-D3 fusion with an affibody that recognizes a specific cell-surface receptor, thereby altering cell-type specificity and functionality. Furthermore, we developed a TGFBR2 nanobody that, on its own, has no inhibitory effect but, when fused to a receptor antibody, antagonizes TGF{beta} signaling in a cell-selective manner. Thus, we designed programmable agents that modulate TGF{beta} signaling only in target co-receptor-expressing cells.

biochemistry↗

bioRxiv2025

THE NSL COMPLEX PROMOTES NEURAL DEVELOPMENT BY PREVENTING R-LOOP INDUCED REPLICATION STRESS

Early neuronal development relies on the proliferation of neural progenitor cells, making this developmental stage particularly vulnerable to DNA replication impediments. Here, we identify a non-canonical role for the non-specific lethal (NSL) complex in safeguarding DNA replication during neurodevelopment. The NSL complex, which acetylates histone 4 at gene promoters and is mutated in Koolen-de Vries syndrome (KdVS), prevents unscheduled R-loop accumulation at weakly transcribed promoters that are typically devoid of R-loops. Single-cell sequencing reveals that loss of NSL causes replisome stalling and delayed S-phase progression. Neural organoids derived from KdVS patients exhibit impaired DNA replication, developmental abnormalities, and reduced synapse formation, driven entirely by unscheduled R-loop accumulation. These findings reveal that faithful DNA replication is critical for early neurodevelopment.

genomics↗

bioRxiv2025

PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single experimental workflow.

Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are common approaches to characterize the genomic localization and protein interactors, respectively, for a protein of interest. However, these approaches require the use of specific antibodies, which often face sensitivity and specificity issues. Based on TurboID, we developed PLAMseq (Proximity Labelled Affinity-purified Mass spectrometry plus sequencing), which enables, in the same workflow, to identify the genomic loci and the interacting proteome of a protein of interest. Moreover, PLAMseq can also be applied to specifically map protein interactions and ubiquitin(-like) modified proteins. We validated PLAMseq with two well characterized proteins, RNA polymerase II and CTCF, with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize Histone H1 SUMOylation, which study has remained elusive due to the lack of specific reagents, and found that SETDB1 binds to SUMOylated histone H1.2 and H1.4 which also colocalize with H3K9me3 at repetitive regions of the genome.

molecular biology↗

bioRxiv2023

Immunometabolic reprogramming by LRH-1/NR5A2 pharmacological activation resolves inflammation in immune cells of type 1 diabetes mellitus individuals and improves human islet engraftment and function

The intricate etiology of type 1 diabetes mellitus (T1D), marked by a detrimental cross-talk between the immune system and insulin-producing {beta}-cells, has impeded effective disease-modifying therapies. The discovery that pharmacological activation of the nuclear receptor LRH-1/NR5A2 can reverse hyperglycemia in mouse models of T1D by attenuating the autoimmune attack coupled to {beta}-cell survival/regeneration, prompted us to investigate whether immune tolerization could be achieved in individuals with T1D by LRH-1/NR5A2 activation as well as improving islet function/survival after xenotransplantation in mice. Pharmacological activation of LRH-1/NR5A2 induced a coordinated genetic and metabolic reprogramming of T1D macrophages and dendritic cells, shifting them from a pro-to an anti-inflammatory/tolerogenic phenotype. Regulatory T-cells were also expanded resulting in the impediment of cytotoxic T-cell proliferation. LRH-1/NR5A2 activation enhanced human islet engraftment and function in hyperglycemic immunocompetent mice. In summary our findings demonstrate the feasibility of re-establishing immune tolerance within a pro-inflammatory environment, opening a new therapeutic venue for T1D.

cell biology↗