Biology subjects

Chavez, S.

Publications and source records attributed to Chavez, S..

16 recordsLinked to original sources

bioRxiv2026

Endogenous mutational mechanisms and metabolic context shape endometrial cancer

Uterine corpus endometrial carcinoma (UCEC) is a common gynecologic malignancy with rising mortality, yet its genome-wide mutational architecture remains incompletely understood. Here we analyze deep whole-genome sequencing data from 440 UCEC tumors from The Cancer Genome Atlas, integrated with transcriptomic and clinical data, to define subtype-specific mutational processes and genomic architectures. We uncover pronounced molecular subtype-specific differences in endogenous mutational mechanisms, retrotransposition activity, structural variation, and chromosomal instability. LINE-1 retrotransposition emerges as a key contributor to genome instability in UCEC, acting as a prominent source of structural variation in copy-number stable tumors and associating with chromothripsis and ecDNA-mediated oncogene amplification in copy-number high tumors. Mutational signature SBS28 contributes significantly to mutations in POLE-deficient tumors and is strongly correlated with SBS10a and SBS10b. Mismatch repair-deficient tumors exhibit a previously unrecognized doublet base substitution signature and a defining imbalance between ID2 and ID1 indel processes, reflecting pervasive DNA template-strand replication slippage and associated with increased tumor immunogenicity. Copy-number low tumors follow a distinct low-mutagenesis evolutionary trajectory characterized by reduced replication stress, low proliferative activity, genomic stability and enrichment of SBS18 associated with oxidative damage. Notably, we identify a consistent inverse association between body mass index and tumor mutational burden in UCEC, suggesting that host metabolic state may influence fundamental cellular processes governing mutation accumulation, promoting tumor development through non-mutagenic mechanisms rather than elevated genomic instability. Together, these findings establish a mutagenesis-centric framework for UCEC that links endogenous mutational mechanisms to tumor architecture and host metabolic context, uncovering previously unrecognized subtype-specific genomic features with important implications for refined risk stratification and therapeutic strategies.

genomics↗

bioRxiv2025

Maternal CENP-C restores centromere symmetry in mammalian zygotes to ensure proper chromosome segregation

Across metazoan species, the centromere-specific histone variant CENP-A is essential for accurate chromosome segregation, yet its regulation at the parental-to-zygote transition in mammals is poorly understood. To address this, we developed a CENP-A-mScarlet knock-in mouse model, which revealed sex-specific dynamics: mature sperm retains 10% of the CENP-A levels present in MII-oocytes. However, in zygotes prior to the first mitosis, this difference is resolved, using maternally inherited cytoplasmic-CENP-A. Notably, the increase in CENP-A at paternal centromeres is independent of sensing CENP-A asymmetry or the presence of maternal chromosomes. Instead, CENP-A equalization relies on asymmetric recruitment of maternal CENP-C to paternal centromeres. Depletion of maternal CENP-A decreases total CENP-A in pronuclei without disrupting equalization. In contrast, reducing maternal CENP-C or disruption of its dimerization domains impairs CENP-A equalization and chromosome segregation. Therefore, maternal CENP-C acts a key epigenetic regulator that resets centromeric symmetry at fertilization to preserve genome integrity. Highlights[bullet] CENP-A asymmetry between sperm and oocyte centromeres is a conserved feature from flies to mammals including mice and humans. [bullet]CENP-A asymmetry between parental centromeres is resolved prior to the first zygotic division via maternally inherited, cytoplasmic CENP-A. [bullet]Zygotic CENP-A levels in zygotes are regulated in a pronucleus-autonomous manner. [bullet]CENP-A equalization relies on asymmetric CENP-C recruitment to the paternal pronucleus and requires CENP-C dimerization. Key TermsCentromere; CENP-A; CENP-C; sperm; oocyte; zygote; intergenerational; epigenetics; mouse

genetics↗

bioRxiv2025

Regulation of transcription elongation anticipates alternative gene expression strategies across the cell cycle

A growing body of evidence supports the idea that RNA polymerase II (RNAP II) activity during transcription elongation can be regulated to control transcription rates. Using genomic run-on and RNAP II chromatin immunoprecipitation, we measured both active and total RNAP II across the bodies of genes at three different stages of the mitotic cell cycle in Saccharomyces cerevisiae: G1, S, and G2/M. Comparison of active and total RNAP II levels at these stages revealed distinct patterns of transcription elongation control throughout the cell cycle. Previously characterized cycling genes were associated with some of these elongation patterns. A cluster of genes with highly divergent genomic run-on and RNAP II chromatin immunoprecipitation patterns was notably enriched in genes related to ribosome biogenesis and the structural components of the ribosome. We confirmed that the expression of ribosome biogenesis mRNAs increases after G1 but decreases following mitosis. Finally, we analyzed the contribution of mRNA stability to each cluster and found that a coordinated regulation of RNAP II activity and mRNA decay is necessary to fully understand the alternative strategies of gene expression across the cell cycle.

molecular biology↗

bioRxiv2024

Growth rate regulates RNA polymerase II transcription elongation in Saccharomyces cerevisiae

Cells must adapt to changing environmental conditions to maintain their fitness and to compete with other genotypes during the natural selection process. The growth rate (GR) is a determining factor in this competition, and it influences gene expression. Some genes increase mRNA levels, while others decrease with the GR. mRNA levels depend on the dynamic balance between their synthesis by RNA polymerase II and their degradation rates. RNA polymerase I and III are also influenced by the GR because they transcribe protein synthesis machinery required to make proteins that increase cell mass during growth. Although RNA levels have been extensively studied in relation to the GR in many organisms, synthesis and degradation rates have, however, been much less investigated. In a previous work, we found a positive correlation between RNA polymerase (RNA pol) II transcription and mRNA degradation with GRs in yeast in batch cultures. Here we extend our study under constant growth conditions in a chemostat and find that overall chromatin-associated RNA pol II levels increase in parallel with the GR. This increase appears to involve the accumulation of partially dephosphorylated RNA pol II with a greater tendency to backtracking, which suggests that the GR regulates RNA pol II-dependent transcription at the elongation level. RNA pol I also increases its association with chromatin with the GR, which confirms the general dependence of at least RNA pol I and II transcription on the GR.

molecular biology↗

bioRxiv2023

Boosting bactericidal immunity of a recombinant Mycobacterium smegmatis strain via zinc-dependent ribosomal proteins

Tuberculosis (TB) continues to be a major global health burden and kills over a million people annually. New immunization strategies are required for the development of an efficacious TB vaccine that can potentially induce sterilizing immunity. In this study, we first confirmed that various strains of the IKEPLUS vaccine confer a higher survival benefit than BCG in a murine model of intravenous Mycobacterium tuberculosis (Mtb) infection. We have shown that there was a significant increase in the expression of the Rv0282 when IKEPLUS was grown in low zinc and iron containing Sauton medium. We confirmed on biofilm assays that zinc plays a vital role in the growth and formation of Mycobacterium smegmatis (M. smegmatis) biofilms. IKEPLUS grown in low zinc media led to better protection of mice after intravenous challenge with very high dosage of Mtb. We also showed that various variants of IKEPLUS induced apoptotic cell-death of infected macrophages at a higher rate than wild type M. smegmatis. We next attempted to determine if zinc containing ribosomal proteins such as rpmb2 could contribute to protective efficacy against Mtb infection. Since BCG has an established role in anti-mycobacterial efficacy, we boosted BCG vaccinated mice with rmpb2 but this did not lead to an increment in the protection mediated by BCG.

microbiology↗

bioRxiv2023

Ectopic transcription due to inappropriately inherited histone methylation may interfere with the ongoing function of terminally differentiated cells

How mutations in histone modifying enzymes lead to neurodevelopmental disorders is unknown. We took advantage of the invariant embryonic lineage and adult nervous system in C. elegans to investigate a double mutant between spr-5/Lsd1/Kdm1a (H3K4me1/2 demethylase) and met-2/Setdb1 (H3K9 methyltransferase). We demonstrate that spr-5; met-2 double mutant worms have a severe chemotaxis defect caused by the ectopic expression of germline genes in somatic tissues. Despite this behavioral defect, we observe few embryonic lineage alterations and an intact adult nervous system. This raises the possibility that the abnormal chemotaxis behavior may be due to ongoing defects in terminally differentiated cells rather than alterations in development. Remarkably, we found that shutting off the ectopic germline expression rescues normal chemotaxis in the same spr-5; met-2 adult worms that had a chemotaxis defect earlier. This suggests that ongoing inappropriate transcription can block normal behavior in an intact nervous system. Based on these data, it is possible that the intellectual disability and altered behavior observed in human neurodevelopmental syndromes caused by mutations in histone modifying enzymes could be due to ongoing ectopic transcription and may be reversible.

developmental biology↗

bioRxiv2023

The transcription factor Sfp1 imprints specific classes of mRNAs and links their synthesis and cytoplasmic decay

To function effectively as an integrated system, the transcriptional and post-transcriptional machineries must communicate through mechanisms that are still poorly understood. Here we focus on Sfp1, known to regulate transcription of proliferation-related genes. We show that Sfp1 can regulate transcription either by binding to promoters, like most known transcription activators, or by binding to the transcribed regions (gene bodies), probably via RNA polymerase II (Pol II). We further studied the first mode of Sfp1 activity and found that, following promoter binding, Sfp1 binds to gene bodies and affects Pol II configuration, manifested by dissociation or conformational change of its Rpb4 subunit and increased backtracking. Surprisingly, Sfp1 binds to a subset of mRNAs co-transcriptionally and stabilizes them. The interaction between Sfp1 and its client mRNAs is controlled by their respective promoters and coincides with Sfp1s dissociation from chromatin. . Intriguingly, Sfp1 dissociation from the chromatin correlates with the extent of the backtracked Pol II. We propose that, following promoter recruitment, Sfp1 accompanies Pol II and regulates backtracking. The backtracked Pol II is more compatible with Sfp1s relocation to the nascent transcripts, whereupon Sfp1 accompanies these mRNAs to the cytoplasm and regulates their stability. Thus, Sfp1s co-transcriptional binding imprints the mRNA fate, serving as a paradigm for the cross-talk between the synthesis and decay of specific mRNAs. The interplay between Sfp1s two modes of transcription regulation remains to be examined.

molecular biology↗

bioRxiv2023

Repeated MRI scans of the human brain: diurnal oscillations in healthy adults and bipolar disorder patients

Regulation of biological processes according to a 24-hr rhythm is essential for the normal functioning of an organism. Temporal variation in brain MRI data has often been attributed to circadian or diurnal oscillations; however, it is not clear if such oscillations exist. We provide the first evidence that diurnal oscillations indeed govern multiple MRI metrics. We recorded cerebral blood flow, diffusion-tensor metrics, T1 relaxation, and cortical structural features every three hours over a 24-hr period in each of 16 male controls and eight male bipolar disorder patients. Diurnal oscillations were detected in numerous MRI metrics at the whole-brain level, and regionally. Rhythmicity parameters in the bipolar disorder patients were similar to the controls for most metrics, except for a larger phase variation in cerebral blood flow. The ubiquitous nature of diurnal oscillations has broad implications for neuroimaging studies and furthers our understanding of the dynamic nature of the human brain.

neuroscience↗

bioRxiv2023

Replicative age negatively influences proliferative capacity since early stages in a Whi5-dependent manner

Clonal populations exhibit phenotypic variation despite being composed of genetically identical cells under the same environmental conditions. Proliferation rate also shows this heterogeneity, but the underlying mechanisms remain poorly understood. In this study, we combined single-cell microencapsulation with confocal microscopy to develop a new experimental approach for analyzing budding yeast cell lineages and determining the age of every cell within each microcolony. We found that most slow-growing lineages are founded by young mother cells that have undergone only a few cell divisions, typically between 1 and 4. This reduction in proliferative capacity is linked to the expression levels of the cell cycle regulator Whi5, which increase with the number of replication cycles, even since the earliest stages. We also found that the increased levels of Whi5 are due to the higher accumulation of its mRNA during the S/G2/M phases of young mother cells compared to newborn cells. Our results show that the proliferative structure of a cell population is progressively shaped in each mitotic cycle, starting from the very first division, when a mother cell has the opportunity to establish a slow proliferating lineage. Possible mechanisms of Whi5 action to mediate this effect are discussed.

molecular biology↗

bioRxiv2023

The association of the RSC remodeler complex with chromatin depends on prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae

The tripartite interaction between the chromatin remodeler complex RSC, RNA polymerase subunit Rpb5 and prefoldin-like Bud27 is necessary for proper RNA pol II elongation. Indeed lack of Bud27 alters this association and affects transcription elongation. This work investigates the consequences of lack of Bud27 on the chromatin association of RSC and RNA pol II, and on nucleosome positioning. Our results demonstrate that RSC binds chromatin to gene bodies and lack of Bud27 alters this association, mainly around polyA sites. This alteration impacts chromatin organization and leads to the accumulation of RNA pol II molecules around polyA sites, likely to be arrested or slower. Our data suggest that RSC is necessary to maintain chromatin organization around those sites, and any alteration of this organization results in the widespread use of alternative polyA sites. Finally, we also find a similar molecular phenotype that occurs upon TOR inhibition with rapamycin, which suggests that alternative polyadenylation observed upon TOR inhibition is likely Bud27-dependent.

molecular biology↗

bioRxiv2022

Gene regulation by synergism between mRNA decay and gene transcription

It has become increasingly clear in the last few years that gene expression in eukaryotes is not a linear process starting from transcription in the nucleus to the cytoplasm, but a circular one where the mRNA level is controlled by crosstalk between nuclear transcription and cytoplasmic decay pathways. One of the possible purposes of this crosstalk is to keep the mRNA level approximately constant. This is called mRNA buffering and happens when transcription and mRNA degradation act at compensatory rates. However, if transcription and mRNA degradation act synergistically, enhanced gene expression regulation would occur. In this work we mathematically modeled the effects of RNA binding proteins (RBP) when they have positive or negative effects on mRNA synthesis and decay rates. We found that they can buffer or enhance gene expression responses depending on their respective effects on transcription and mRNA stability. Then we analyzed new and previously published genomic datasets obtained for several yeast mutants related to either transcription or mRNA decay, but they are not known to possess activity in the other process. We show that some of them, which were presumed only transcription factors (Sfp1) or only decay factors (Puf3, Upf2/3), may represent examples of RBPs that make specific synergistic crosstalk to enhance the control of the mRNA levels of their target genes by combining antagonistic effects on transcriptional and mRNA stability.

molecular biology↗

bioRxiv2021

The total mRNA concentration buffering system in yeast is global rather than gene-specific

Gene expression in eukaryotes does not follow a linear process from transcription to translation and mRNA degradation. Instead it follows a circular process in which cytoplasmic mRNA decay crosstalks with nuclear transcription. In many instances this crosstalk contributes to buffer mRNA at a roughly constant concentration. Whether the mRNA buffering concept operates on the total mRNA concentration or at the gene-specific level, and if the mechanism to do so is a global or a specific one, remain unknown. Here we assessed changes in mRNA concentrations and their synthesis rates along the transcriptome of aneuploid strains of the yeast Saccharomyces cerevisiae. We also assessed mRNA concentrations and their synthesis rates in non sense-mediated decay (NMD) targets in euploid strains. We found that the altered synthesis rates in the genes from the aneuploid chromosome and the changes in their mRNA stabilities were not counterbalanced. In addition, the stability of NMD targets was not specifically compensated by the changes in synthesis rate. We conclude that there is no genetic compensation of NMD mRNA targets in yeast, and total mRNA buffering uses mostly a global system rather than a gene-specific one.

molecular biology↗

bioRxiv2020

Human Prefoldin Modulates Co-transcriptional Pre-mRNA Splicing

Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.

molecular biology↗

bioRxiv2020

Xrn1 influences RNA pol II-dependent transcription elongation rates across the yeast genome and this control is particularly relevant for late elongation of regulatory genes

mRNA homeostasis is favored by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5 exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3 was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favoring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.

genomics↗

bioRxiv2020

An overview of the quality assurance and quality control of magnetic resonance imaging data for the Ontario Neurodegenerative Disease Research Initiative (ONDRI): pipeline development and neuroinformatics

Large scale research studies combining magnetic resonance imaging data generated at multiple sites on multiple vendor platforms are becoming more commonplace. The Ontario Neurodegenerative Disease Research Initiative (ONDRI - http://ondri.ca/), a project funded by the Ontario Brain Institute (OBI), is a recently established province-wide natural history study, which has recruited more than 500 participants from neurodegenerative disease groups including amyotrophic lateral sclerosis, fronto-temporal dementia, Parkinsons disease, Alzheimers disease, mild cognitive impairment, and cerebrovascular disease (previously referred to as the vascular cognitive impairment cohort). Because of its multi-site nature, all captured data must be standardized and meet minimum quality standards to reduce variability. The goal of the ONDRI imaging platform is to maximize data quality by implementing vendor-specific harmonized MR imaging protocols (consistent with the Canadi-an Dementia Imaging Protocol - http://www.cdip-pcid.ca/), monitoring protocol adherence, qualitatively assessing image quality, measuring signal-to-noise and contrast-to-noise, monitoring system stability, and applying corrections based on the analysis of images from two different phantoms regularly acquired at each site. To maximize image quality, this work describes the use of various automatic pipelines and manual assessment steps, integrated within an established informatics and databasing platform, the Stroke Patient Recovery Research Database (SPReD) built on the Extensible Neuroimaging Archive Toolkit (XNAT), and contained within the Brain-CODE (Centre for Ontario Data Exploration) framework. The purpose of the current paper is to describe the steps undertaken by ONDRI to achieve this high standard of data integrity. Data have been successfully collected for the past 4 years with the pipelines and assessments identifying deviations, allowing for timely interventions and assessment of image quality.

neuroscience↗

bioRxiv2019

Homeostasis in the Central Dogma of Molecular Biology

Cell survival requires the control of biomolecule concentration, i.e. biomolecules should approach homeostasis. With information-carrying macromolecules, the particular concentration variation ranges depend on each type: DNA is not buffered, but mRNA and protein concentrations are homeostatically controlled, which leads to the ribostasis and proteostasis concepts. In recent years, we have studied the particular features of mRNA ribostasis and proteostasis in the model organism S. cerevisiae. Here we extend this study by comparing published data from three other model organisms: E. coli, S. pombe and cultured human cells. We describe how mRNA ribostasis is less strict than proteostasis. A constant ratio appears between the average decay and dilution rates during cell growth for mRNA, but not for proteins. We postulate that this is due to a trade-off between the cost of synthesis and the response capacity. This compromise takes place at the transcription level, but is not possible at the translation level as the high stability of proteins, versus that of mRNAs, precludes it. We hypothesize that the middle-place role of mRNA in the Central Dogma of Molecular Biology and its chemical instability make it more suitable than proteins for the fast changes needed for gene regulation.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC=\"FIGDIR/small/599050v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (24K):\norg.highwire.dtl.DTLVardef@95419aorg.highwire.dtl.DTLVardef@10612e5org.highwire.dtl.DTLVardef@1c29081org.highwire.dtl.DTLVardef@9d21c0_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

molecular biology↗