Biology subjects

Garrido, C.

Publications and source records attributed to Garrido, C..

12 recordsLinked to original sources

bioRxiv2026

Centromeric origin of Arabidopsis interstitial telomeric repeat domains

The mechanisms underlying the emergence of new DNA repeat classes remain poorly understood. One such example is the formation of interstitial telomeric repeat (ITR) domains commonly viewed as telomere-fossil byproducts of chromosome rearrangements. Here, we report that in Arabidopsis thaliana, ITRs arise from centromeres as centromeric-telomeric mosaic satellites that expand into higher-order structures via in situ amplification. Long-read sequencing of mutation accumulation lines and forward simulations of mutational processes confirmed the propensity of centromeres to form telomeric motifs. During establishment, ITRs adopt an atypical chromatin state that excludes CENH3 incorporation, thereby enabling escape from the functional constraints of centromere identity. Accordingly, a pangenomic survey of natural accessions showed that ITRs vary abruptly and independently of telomere length, notably through transposon-associated block duplications. These findings identify centromeres as major sources of telomeric sequences and an original route for the emergence of new DNA satellite types.

genomics↗

bioRxiv2026

CASM potentiates STING-driven NFκB signaling in immune cells

Stimulator of Interferon Gene (STING), a key player of antimicrobial immune responses, has emerged as a promising target to mitigate inflammation and cancer. Following STING activation, proinflammatory molecules and type I Interferons (IFN) are released thus favoring the establishment of effective immune responses and adaptive immunity. Autophagy has been proposed to negatively regulate STING signaling. While STING activation drives microtubule-associated proteins 1A/1B light chain 3B (hereafter referred to as LC3) lipidation, the underlying mechanisms and functional consequences remain however incompletely defined. Especially, the consequences of STING-associated Conjugation of autophagy related (ATG) 8 to Single Membranes (CASM) in the control of immune responses remain elusive. Using innate and adaptive cells specifically inactivated for autophagy or CASM, we found that STING agonists primarily trigger CASM over autophagy. While STING-associated autophagy exerts negative feedback on the STING pathway and downstream type I IFN and pro-inflammatory responses, with different underlying molecular mechanisms between immune cells, STING-driven CASM potentiates NF{kappa}B-associated TNF production. These results overall uncover a new function of CASM and underscore the relevance of both CASM and autophagy in shaping STING signaling

cell biology↗

bioRxiv2025

Transient telomere uncapping triggers telomeric and subtelomeric rearrangements

Telomeres are nucleoprotein structures that cap the extremities of eukaryotic linear chromosomes, thus preventing them from being detected as DNA damage. Telomere uncapping poses a profound threat to genome integrity, yet the immediate consequences of transient uncapping remain unclear. In Saccharomyces cerevisiae, the Cdc13-Stn1-Ten1 complex caps telomeres and limits resection, which would otherwise lead to DNA damage checkpoint activation. Here, using the temperature-sensitive cdc13-1 allele, we demonstrate that even transient telomere uncapping induces extensive genomic rearrangements within a few cell cycles, despite a functional DNA damage checkpoint. Two distinct rearrangement signatures were observed in cells surviving transient uncapping: one characterized by the reorganization and recombination of the subtelomeric region, mostly involving the Y elements, and the other exhibiting massively elongated telomeres up to 10 kb, corresponding to a [~]30-fold increase. Long-read sequencing revealed that the genomic instability was confined to the subtelomere and telomere regions, and evidenced Y' element loss/amplification, terminal duplication of chromosome ends, and telomeric-circle-driven amplification of telomere repeats. Rearrangements unfold over multiple generations and require the homologous recombination factor Rad52 and the Pol{delta} subunit Pol32, which is essential for break-induced replication. The recombination proteins Rad51 and Rad59 also contribute to the rearrangements in partially independent pathways. Remarkably, survivors with elongated telomeres demonstrate robust resistance to subsequent telomere uncapping, in a Rad52-dependent manner. Our findings provide novel insights into the consequences of transient telomere uncapping for genome stability, a process that might contribute to subtelomere and telomere dynamics and evolution.

molecular biology↗

bioRxiv2025

Natural diversity of telomere length distributions across 100 yeast strains

Telomeres gradually shorten at each cell division and telomerase counteracts this shortening by elongating telomere sequences. This dynamic balance between elongation and shortening results in a steady-state telomere length (TL) distribution. We developed a method for detecting telomeric sequences in Saccharomyces cerevisiae genomes from raw Oxford Nanopore Technologies (ONT) sequencing reads, providing a comprehensive view of TL distributions both genome-wide and at individual chromosome extremities. We analyzed the TL distribution in 100 S. cerevisiae strains, representing the genetic and ecological diversity of the species. Our analysis revealed a large diversity in TL distributions within the species, largely driven by inter-extremity differences, ploidy level, and subtelomere structure. Polyploid strains displayed significantly longer telomeres than diploid and haploid strains, and experiments with artificially generated polyploids in two independent genetic backgrounds confirmed that higher ploidy levels lead to telomere elongation. Furthermore, we found that the subtelomeric Y element exerts two distinct and opposing effects: (i) the presence of Y elements at a chromosome extremity is associated with shorter telomeres in cis, but (ii) the overall Y element content in a strain correlates with longer telomeres. Interestingly, the length of the shortest telomeres remained relatively constant across strains, suggesting a selective constraint at the species level. This study reveals the diversity of TL in S. cerevisiae and highlights key factors shaping TL distributions both genome-wide and at individual chromosome extremities.

genomics↗

bioRxiv2023

Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1

Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy. Current research efforts to cure HIV-1 infection include "shock and kill" strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells. The modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy. Aminobisphosphonates (N-BPs) that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies. Here, we show the use of N-BPs as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that N-BPs induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin (PHA). RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further evidence of alendronate-mediated latency reversal and activation of immune effector cells. Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of N-BPs to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.

microbiology↗

bioRxiv2023

Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii

Telomeres and subtelomeres, the genomic regions located at chromosome extremities, are essential for genome stability in eukaryotes. In the absence of the canonical maintenance mechanism provided by telomerase, telomere shortening induces genome instability. The landscape of the ensuing genome rearrangements is not accessible by short-read sequencing. Here, we leverage Oxford Nanopore Technologies long-read sequencing to survey the extensive repertoire of genome rearrangements in telomerase mutants of the model green microalga Chlamydomonas reinhardtii. In telomerase mutant strains grown for [~]700 generations, most chromosome extremities were capped by short telomere sequences that were either recruited de novo from other loci or maintained in a telomerase-independent manner. Other extremities did not end with telomeres but only with repeated subtelomeric sequences. The subtelomeric elements, including rDNA, were massively rearranged and involved in breakage-fusion-bridge cycles, translocations, recombinations and chromosome circularization. These events were established progressively over time and displayed heterogeneity at the subpopulation level. New telomere-capped extremities composed of sequences originating from more internal genomic regions were associated with high DNA methylation, suggesting that de novo heterochromatin formation contributes to restore chromosome end stability in C. reinhardtii. The diversity of alternative strategies to maintain chromosome integrity and the variety of rearrangements found in telomerase mutants are remarkable and illustrate genome plasticity at short timescales.

genomics↗

bioRxiv2022

p16High senescence restricts totipotent potential during somatic cell reprogramming

The discovery of four factor (4F)-induced reprogramming of somatic cells into induced pluripotent stem (iPS) cells has revolutionized the fields of cell and regenerative biology. In contrast, the feasibility of a direct conversion of somatic cells into a totipotent state defined as the ability to produce all cell types of an organism, including extraembryonic tissues, is not well established. Using genetic and chemical approaches to manipulate senescent cells, here we found that removal of p16High cells resulted in 4F-induced reprogramming of somatic cells into totipotent-like stem cells. These cells expressed markers of both pluripotency and the 2-cell (2C) embryonic state, readily formed implantation-competent blastocyst-like structures, blastoids, and following morula aggregation, contributed to embryonic and extraembryonic lineages in E12.5 embryos. We identified senescence-dependent regulation of nicotinamide N-methyltransferase (NNMT) as a key mechanism controlling the S-adenosyl-O_SCPLOWLC_SCPLOW-methionine (SAM) levels during 4F-induced reprogramming that was required for expression of the 2C genes and acquisition of an extraembryonic potential. Our results show that the presence of p16High senescent cells, high NNMT and low SAM limit cell plasticity during 4F-reprogramming, while their modulation could help to achieve the highest state of stem cell potency, totipotency.

cell biology↗

bioRxiv2022

Distinct upper airway epithelium interferon-stimulated and profibrotic gene expression between adult and infant rhesus macaques infected with SARS-CoV-2

The global spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its associated coronavirus disease (COVID-19) has led to a pandemic of unprecedented scale. An intriguing feature of the infection is the minimal disease in most children, a demographic at higher risk for respiratory viral diseases. To elucidate age-dependent effects of SARS-CoV-2 pathogenesis, we inoculated two rhesus macaque monkey dam-infant pairs with SARS-CoV-2 and conducted virological and transcriptomic analysis of the respiratory tract and evaluated systemic cytokine and antibody responses. Viral RNA levels in all sampled mucosal secretions were comparable across dam-infant pairs in the respiratory tract. Despite comparable viral loads, adult macaques showed higher IL-6 in serum while CXCL10 was induced in all animals. Both groups mounted neutralizing antibody (nAb) responses, with infants showing a more rapid induction at day 7. Transcriptome analysis of tracheal tissue isolated at day 14 post-infection revealed significant upregulation of multiple interferon-stimulated genes in infants compared to adults. In contrast, a profibrotic transcriptomic signature with genes associated with cilia structure and function, extracellular matrix (ECM) composition and metabolism, coagulation, angiogenesis, and hypoxia was induced in adults compared to infants. Our observations suggest age-dependent differential airway responses to SARS-CoV-2 infection that could explain the distinction in pathogenesis between infants and adults.

immunology↗

bioRxiv2021

Retracing the evolution from antimicrobial to targeting peptides

We asked what peptide features govern targeting to the mitochondria versus the chloroplast using antimicrobial peptides as a starting point. This approach was inspired by the endosymbiotic hypothesis that organelle-targeting peptides derive from antimicrobial amphipathic peptides delivered by the host cell, to which organelle progenitors became resistant. To explore the molecular changes required to convert antimicrobial into targeting peptides, we expressed a set of 13 antimicrobial peptides in Chlamydomonas reinhardtii. Peptides were systematically modified to test distinctive features of mitochondrial and chloroplast targeting peptides, and we assessed their targeting potential by following the intracellular localization and maturation of a Venus fluorescent reporter used as cargo protein. Mitochondrial targeting can be achieved by some unmodified antimicrobial peptide sequences. Targeting to both organelles is improved by replacing Lysines with Arginines. Chloroplast targeting is enabled by the presence of flanking unstructured sequences, additional constraints consistent with chloroplast endosymbiosis having occurred in a cell that already contained mitochondria. If indeed targeting peptides evolved from antimicrobial peptides, required modifications imply a temporal evolutionary scenario with an early exchange of cationic residues, and a late acquisition of chloroplast specific motifs.

evolutionary biology↗

bioRxiv2021

Meditation-induced effects on whole-brain structural and effective connectivity

In the past decades, there has been a growing scientific interest in characterizing neural correlates of meditation training. Nonetheless, the mechanisms underlying meditation remain elusive. In the present work, we investigated meditation-related changes in structural and functional connectivities (SC and FC, respectively). For this purpose, we scanned experienced meditators and control (naive) subjects using magnetic resonance imaging (MRI) to acquire structural and functional data during two conditions, resting-state and meditation (focused attention on breathing). In this way, we aimed to characterize and distinguish both short-term and long-term modifications in the brains structure and function. First, we performed a network-based analysis of anatomical connectivity. Then, to analyze the fMRI data, we calculated whole-brain effective connectivity (EC) estimates, relying on a dynamical network model to replicate BOLD signals spatio-temporal structure, akin to FC with lagged correlations. We compared the estimated EC, FC, and SC links as features to train classifiers to predict behavioral conditions and group identity. The whole-brain SC analysis revealed strengthened anatomical connectivity across large-scale networks for meditators compared to controls. We found that differences in SC were reflected in the functional domain as well. We demonstrated through a machine-learning approach that EC features were more informative than FC and SC solely. Using EC features we reached high performance for the condition-based classification within each group and moderately high accuracies when comparing the two groups in each condition. Moreover, we showed that the most informative EC links that discriminated between meditators and controls involved the same large-scale networks previously found to have increased anatomical connectivity. Overall, the results of our whole-brain model-based approach revealed a mechanism underlying meditation by providing causal relationships at the structure-function level.

neuroscience↗

bioRxiv2019

Characterizing the dynamical complexity underlying meditation

Over the past 2,500 years, contemplative traditions have explored the nature of the mind using meditation. More recently, neuroimaging research on meditation has revealed differences in brain function and structure in meditators. Nevertheless, the underlying neural mechanisms are still unclear. In order to understand how meditation shapes global activity through the brain, we investigated the spatiotemporal dynamics across the whole-brain functional network using the Intrinsic Ignition Framework. Recent neuroimaging studies have demonstrated that different states of consciousness differ in their underlying dynamical complexity, i.e., how the broadness of communication is elicited and distributed through the brain over time and space. In this work, controls and experienced meditators were scanned using functional magnetic resonance imaging (fMRI) during resting-state and meditation (focused attention on breathing). Our results evidenced that the dynamical complexity underlying meditation shows less complexity than during resting-state in the meditator group but not in the control group. Furthermore, we report that during resting-state, the brain activity of experienced meditators showed higher metastability (i.e., a wider dynamical regime over time) than the one observed in the control group. Overall, these results indicate that the meditation state operates in a different dynamical regime than the resting-state.

neuroscience↗

bioRxiv2018

CBP/EP300-dependent acetylation and stabilization of HSF2 are compromised in the rare disorder, Rubinstein-Taybi syndrome

Cells respond to protein-damaging insults by activating heat shock factors (HSFs), key transcription factors of proteostasis. Abnormal HSF protein levels occur in cancer and neurodegenerative disorders, highlighting the importance of the tight control of HSF expression. HSF2 is a short-lived protein, but it is abundant in the prenatal brain cortex and required for brain development. Here, we reveal that HSF2 is acetylated and co-localized with the lysine-acetyl transferases CBP and EP300 in human brain organoids. Using unbiased, biochemical, cell-imaging, and in silico approaches, we show that CBP/EP300 acetylates HSF2 at specific lysine residues, which promotes HSF2 stabilization, whereas the lysine deacetylase HDAC1 catalyzes its proteasomal degradation. The CBP KIX domain and KlX-recognizing motifs in HSF2 are critical for its interaction with acetylating enzymes. The functional importance of acetylated HSF2 is evidenced in Rubinstein-Taybi syndrome (RSTS), characterized by mutated CBP or EP300. We show that RSTS patient cells exhibit decreased HSF2 levels and impaired heat shock response. The dysregulated HSF pathway in RSTS opens new avenues for understanding the molecular basis of this multifaceted pathology.

developmental biology↗