Biology subjects

Espejo-Serrano, C.

Publications and source records attributed to Espejo-Serrano, C..

6 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

Molecular architecture of meiotic pro-crossover factor HEI10 reveals coupling of higher-order assembly and ubiquitin chain formation

In meiosis, crossovers between homologous chromosomes generate genetic diversity and are required for accurate chromosome segregation, ensuring fertility. In mammals, HEI10 is one of three pro-crossover RING-domain factors implicated in protein modification by ubiquitin and/or SUMO and characterised by their dynamic accumulation at future crossover sites. However, the molecular architecture and enzymatic activity of mammalian HEI10 have remained unknown. Here, we show that human HEI10 has E3-ubiquitin ligase activity that depends on its higher-order assembly. We report the crystal structure of the HEI10 core, revealing how a 29-nm rod-like tetramer is formed through head-to-head association of two coiled-coil dimers that results in clustering of four RING domains around the molecular centre. HEI10 tetramers self-assemble through RING, coiled-coil, and C-terminal interfaces into fibrous and spherical higher-order structures. Structure-guided mutants show that higher-order assembly is required for HEI10 to catalyse K63-linked ubiquitin chain formation in vitro, with the most active species likely corresponding to a loose, non-fibrous network of assembled HEI10 molecules. Arabidopsis thaliana HEI10 retains the tetrameric core and higher-order assembly behaviour, suggesting a conserved principle of HEI10 function.

biochemistry↗

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

Specific genomic targeting of the RNF12/RLIM E3 ubiquitin ligase selectively programmes developmental transcription

The E3 ubiquitin ligase RNF12/RLIM controls developmental gene expression and is mutated in the X-linked intellectual disability disorder Tonne-Kalscheuer syndrome (TOKAS). However, the mechanisms by which RNF12 E3 ubiquitin ligase activity controls specific gene expression signatures are not known. Here, we show that chromatin forms a regulatory platform for RNF12 substrate ubiquitylation and transcriptional patterning. RNF12 is recruited to specific genomic regions via a distinct consensus sequence motif, which enables targeting to key transcription factor substrate REX1. Mechanistically, RNF12 chromatin recruitment is largely REX1 independent, but is achieved via the conserved basic region (BR) adjacent to the RING domain. This region is critical for REX1 ubiquitylation on chromatin and downstream RNF12-dependent gene regulation. Furthermore, we find that RNF12 N-terminal sequences suppress chromatin recruitment and substrate ubiquitylation, uncovering a previously unappreciated autoinhibitory mechanism that governs genome targeting. Taken together, our results provide insight into mechanisms by which selective substrate targeting of an E3 ubiquitin ligase enables specific programming of gene expression.

cell biology↗

bioRxiv2022

Cell autonomous requirement of imprinted XCI inextra-embryonic polar trophoblast cells

In female mice the gene dosage from X chromosomes is adjusted by a process called X chromosome inactivation (XCI) that occurs in two steps. An imprinted form of XCI (iXCI) silencing the paternally inherited X chromosome (Xp) is initiated at the 2-4 cell stages. As extraembryonic cells including trophoblasts keep the Xp silenced, epiblast cells that give rise to the embryo proper reactivate the Xp and undergo a random form of XCI (rXCI) during peri-implantation stages. Lack of X dosage compensation leads to peri-implantation lethality due to inhibition of trophoblast stem cells. However, as the epiblast regulates the trophoblast lineage, the roles of iXCI vs rXCI in the early lethal phenotype remains unclear. We have investigated functions and expression of Rlim (Rnf12), an E3 ubiquitin ligase, and its target protein Rex1 (Zfp42) that control iXCI. Consistent with functions specifically for iXCI, we show an inverse correlation in the expression of Rlim and Rex1 throughout pre-implantation development, but an Rlim-independent downregulation of Rex1 in epiblast cells upon implantation. Moreover, disturbing the functional Rlim-Rex1 dynamics in females leads to cell fate confusion and premature differentiation specifically of the polar trophoblast stem cell pool. Thus, controlled by the Rlim-Rex1 axis, female mouse development requires iXCI in the polar trophoblast cell lineage.

developmental biology↗

bioRxiv2020

A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne-Kalscheuer syndrome

Tonne-Kalscheuer syndrome (TOKAS) is an X-linked intellectual disability syndrome associated with variable clinical features including craniofacial abnormalities, hypogenitalism and diaphragmatic hernia. TOKAS is caused exclusively by variants in the gene encoding the E3 ubiquitin ligase gene RLIM, also known as. Here we report identification of a novel RLIM missense variant, c.1262A>G p.(Tyr421Cys) adjacent to the regulatory basic region, which causes a severe form of TOKAS resulting in perinatal lethality by diaphragmatic hernia. Inheritance and X-chromosome inactivation patterns implicate RLIM p.(Tyr421Cys) as the likely pathogenic variant in the affected individual and within the kindred. We show that the RLIM p.(Tyr421Cys) variant disrupts both expression and function of the protein in an embryonic stem cell model. RLIM p.(Tyr421Cys) is correctly localised to the nucleus, but is readily degraded by the proteasome. The RLIM p.(Tyr421Cys) variant also displays significantly impaired E3 ubiquitin ligase activity, which interferes with RLIM function in Xist long-non-coding RNA induction that initiates imprinted X-chromosome inactivation. Our data uncover a highly disruptive missense variant in RLIM that causes a severe form of TOKAS, thereby expanding our understanding of the molecular and phenotypic spectrum of disease severity.

developmental biology↗