Biology subjects

Ruiz, J. F.

Publications and source records attributed to Ruiz, J. F..

3 recordsLinked to original sources

bioRxiv2024

SCAN1 mutant TDP1 blocks the repair of DSB induced by TOP1 activity during gene transcription and promotes genome reorganisations and cell death in quiescent cells

DNA single-strand breaks (SSBs) are the most common type of DNA damage in quiescent cells, and defects in their repair can lead to hereditary neurological syndromes. A potential endogenous source of SSBs with pathogenic potential is the abortive activity of DNA topoisomerase 1 (TOP1) during transcription. Spinocerebellar ataxia with axonal neuropathy type 1 (SCAN1), is caused by the homozygous mutation H493R in the gene encoding tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that initiates the repair of TOP1-induced SSBs by unlinking the TOP1 peptide from the break end. Notably, transcription-associated TOP1-induced SSBs can be converted into DNA double strand breaks (DSBs) in quiescent cells, with TDP1 also initiating the repair of these breaks. However, the role of TOP1-induced DSBs in the pathology of SCAN1 remains unclear. In this study, we have addressed the impact that SCAN1/H493R mutation, has in the repair of TOP1-induced DSB in quiescent cells. Here we demonstrate that while TDP1 deficiency delays the repair of these breaks, TDP1H493R completely blocks it. This blockage is accompanied by prolonged covalent trapping of TDP1H493R to DNA and results in genome instability and increased cell death in quiescent cells. We also demonstrate that tyrosyl-DNA phosphodiesterase 2 (TDP2) can backup TDP1 loss but not SCAN1 TDP1H493R mutation. Intriguingly, we also unveil that a mutation in catalytic H263 results in a negative dominant effect on TOP1-induced DSB repair. Collectively, our data provide novel insights into the molecular etiology of SCAN1 and support the potential of TOP1-induced DSBs as a main contributor to hereditary neurological syndromes.

genetics↗

bioRxiv2020

RanBP2-mediated SUMOylation promotes human DNA polymerase lambda nuclear localization and DNA repair

Cellular DNA is under constant attack by a wide variety of agents, both endogenous and exogenous. To counteract DNA damage, human cells have a large collection of DNA repair factors. Among them, DNA polymerase lambda (Pol{lambda}) stands out for its versatility, as it participates in different DNA repair and damage tolerance pathways in which gap-filling DNA synthesis is required. In this work we show that human Pol{lambda} is conjugated with Small Ubiquitin-like MOdifier (SUMO) proteins both in vitro and in vivo, with Lys27 being the main target of this covalent modification. Pol{lambda} SUMOylation takes place in the nuclear pore complex and is mediated by the E3 ligase RanBP2. This post-translational modification promotes Pol{lambda} entry into the nucleus, which is required for its recruitment to DNA lesions and stimulated by DNA damage induction. Our work represents an advance in the knowledge of molecular pathways that regulate cellular localization of human Pol{lambda}, which are essential to be able to perform its functions during repair of nuclear DNA, and that might constitute an important point for the modulation of its activity in human cells.

biochemistry↗

bioRxiv2018

Chromatin changes induced by a Plasmodium falciparum infection in Anopheles gambiae

Infection by the human malaria parasite leads to important changes in mosquito phenotypic traits related to vector competence. However, we still lack a clear understanding of the underlying mechanisms and in particular, of the epigenetic basis for these changes. We have examined genome-wide distribution maps of H3K27ac, H3K9ac, H3K9me3 and H3K4me3 by ChIP-seq and the transcriptome by RNA-seq, of midguts from Anopheles gambiae mosquitoes infected with natural isolates of the human malaria parasite Plasmodium falciparum in Burkina Faso. We report 15,916 regions containing differential histone modification enrichment, of which 8,339 locate at promoters and/or intersect with genes. The functional annotation of these regions allowed us to identify infection responsive genes showing differential enrichment in various histone modifications, such as CLIP pro-teases, anti-microbial peptides encoding genes, and genes related to melanization responses and the complement system. Further, the motif analysis of regions differentially enriched in various histone modifications predicts binding sites that might be involved in the cis-regulation of these regions such as Deaf1, Pangolin and Dorsal transcription factors (TFs). Some of these TFs are known to regulate immunity gene expression in Drosophila and are involved in the Notch and JAK/STAT signaling pathways. The analysis of malaria infection-induced chromatin changes in mosquitoes is important not only to identify regulatory elements and genes underlying mosquito responses to a P. falciparum infection but also for possible applications to the genetic manipulation of mosquitoes and to other mosquito-borne systems.

molecular biology↗