Biology subjects

Quiroz, D.

Publications and source records attributed to Quiroz, D..

3 recordsLinked to original sources

bioRxiv2025

Evolutionary trajectories of cohesin gatekeepers across the Tree of Life

Eukaryotic genomes are physically organized into chromatin, which regulates virtually every dimension of genome biology, including replication, recombination, transcription, and DNA repair. Precocious Dissociation of Sisters 5 (PDS5) protein is a key regulator of the cohesin complex, responsible for generating higher-order chromatin structures within and between chromosomes. In yeast and vertebrates, PDS5 can lead to cohesin establishment or disassembly, depending on its interaction with other proteins. In this study, we explored the diversity of PDS5 proteins across eukaryotes; HEAT-repeats forming a hook-like structure (PDS5 domain), followed by a predicted disordered region of variable lengths, are observed across the Tree of Life. Interestingly, two homolog types (A and B) with signs of varying chromatin localization emerged independently in later branches of animal and plant kingdoms, in vertebrates and vascular plants, respectively ([~]400-500 MYA). We also investigated the emergence of two plant-specific features in the PDS5 proteins: 1.) An ancestral acquisition of a Tudor domain with conserved H3K4me1-binding amino acids in land plants 2.) A truncated version of PDS5 proteins that lacks essential features of PDS5 domain and is involved in the RNA-directed DNA methylation (RdDM) plant-specific pathway which emerged in seed plants. This work provides the most comprehensive study of PDS5 diversity, and suggests the emergence of specialized cohesin regulatory mechanisms that could shape distinct strategies for genome organization across eukaryotes. Short summaryHere, we analyzed the diversification of PDS5 proteins; sequence, domain content, and structure, providing new observations that evidence different evolutionary trajectories of this protein across the Tree of Life. These results suggest neofunctional evolution in cohesin regulatory proteins that could shape distinct strategies for genome organization across eukaryotes.

evolutionary biology↗

bioRxiv2022

Relationship between biased mutagenesis and H3K4me1-targeted DNA repair in plants

Mutation is the ultimate source of genetic variation. Mutation rate variability has been observed within plant genomes, but the underlying mechanisms have been unclear. We previously found that mutations occur less often in functionally constrained regions of the genome in Arabidopsis thaliana and that this mutation rate reduction is predicted by H3K4me1, a histone modification found in the gene bodies of actively expressed and evolutionarily conserved genes in plants. We reanalyzed de novo germline single base substitutions in fast neutron irradiated mutation accumulation lines in Kitaake rice (Oryza sativa) and found the same reduction in mutations associated with H3K4me1, gene bodies, and constrained genes as in A. thaliana, suggesting conserved mechanisms for mutation reduction in plants. Here, we characterize a model of targeted DNA repair to explain these observations; PDS5C and MSH6 DNA repair-related proteins target H3K4me1 through their Tudor domains, resulting in nearby DNA experiencing elevated repair. Experimental data and in-silico modeling support the high affinity of the Tudor domain for H3K4me1 in both proteins, and that this affinity is conserved between plant species. ChIP-seq data from PDS5C confirms its localization to conserved and low mutation rate genome regions. Somatic and germline mutations observed by deep sequencing of wild-type and MSH6 knockout lines confirm that MSH6 preferentially repairs gene bodies and H3K4me1-enriched regions. These findings inspire further research to characterize the origins of mechanisms of targeted DNA repair in eukaryotes and their consequences on tuning the evolutionary trajectories of genomes.

genomics↗

bioRxiv2021

Rootstocks influence the response of ripening grape berries to leafroll associated viruses

Grapevine leafroll-associated virus (GLRaV) infections are accompanied by symptoms with varying severity. Using a dedicated experimental vineyard, we studied the responses to GLRaVs in ripening berries from Cabernet franc grapevines grafted to different rootstocks and with zero, one, or pairs of leafroll infection(s). RNA sequencing data were mapped to a high-quality Cabernet franc genome reference assembled to carry out this study and integrated with hormone and metabolite abundance data. This study identified several molecular levers that participate in responses to GLRaVs, including those that are condition-dependent. This included describing common responses to GLRaVs that were reproduced in two consecutive years, in plants grafted to different rootstocks, and in more than one infection condition. Though different infections were inconsistently distinguishable from one another overall, the effects of infections in plants grafted to different rootstocks were distinct at each developmental stage. Conserved responses included the modulation of pathogen detecting genes, increases in abscisic acid signaling and cytoskeleton remodeling gene expression. The abundance of abscisic acid (ABA), related metabolites, ABA and hormone signaling-related gene expression, and the expression of several transcription factor families differentiated rootstocks overall. These data show that rootstock influences the effect of GLRaVs in ripening berries.

plant biology↗