Biology subjects

Oliveira, R. A.

Publications and source records attributed to Oliveira, R. A..

14 recordsLinked to original sources

bioRxiv2026

Distinct regulation across the transcription cycle drives mitotic transcriptional silencing

In most organisms, as cells enter mitosis, transcription is globally silenced. While individual studies have shown that each stage of the transcription cycle can be modulated during mitosis, how initiation, elongation, and termination are temporally and kinetically regulated to ensure transcriptional silencing remains unclear. Here, we combine real-time quantitative imaging of ongoing transcription in early Drosophila embryos with mathematical modelling to systematically dissect how transcriptional kinetics change as cells progress into mitosis. We found that transcription initiation undergoes a gradual repression starting in prophase, while elongation rates remain unaltered. After nuclear envelope breakdown, an abrupt mechanism causes premature termination of elongating RNA, driven at least in part by the SNF-helicase-like protein Transcription Termination factor 2 / Lodestar (TTF2/Lds). Our study provides a quantitative framework for understanding how transcription is modulated across the cell cycle, demonstrating that mitotic repression arises from multiple processes with different dynamics that collectively ensure the precise shutdown of gene expression.

cell biology↗

bioRxiv2026

DNA catenation is essential for Sister Chromatid Cohesion

From S phase until anaphase, sister chromatids remain physically linked to ensure accurate chromosome segregation. This linkage, called sister chromatid cohesion, must withstand the pulling forces generated by the mitotic spindle and is thought to require entrapment of sister DNAs inside the ring-shaped cohesin complex. DNA catenations that arise naturally during replication could also tether sister chromatids, but whether they contribute to cohesion has remained unresolved. Here, using budding yeast, we show that cohesin-mediated sister DNA entrapment alone cannot withstand spindle-generated pulling forces and that robust sister chromatid cohesion requires DNA catenation. Selective removal of DNA catenations causes catastrophic cohesion loss, delays chromosome biorientation and increases chromosome mis-segregation, even when cohesin rings remain intact. Importantly, DNA catenation similarly underpins force-resistant cohesion in metazoan chromosomes. Our findings fundamentally redefine the physical basis of sister chromatid cohesion by establishing DNA catenation as an evolutionarily conserved component of the force-resistant linkage between sister chromatids that enables accurate chromosome segregation.

molecular biology↗

bioRxiv2026

TTF2 prevents premature rRNA synthesis during mitotic exit

Mitosis poses major challenges to cellular transcription. As cells enter mitosis, transcription is globally silenced and must be precisely restored upon mitotic exit. These processes are primarily regulated by Cdk1-dependent phosphorylation. In parallel, additional mechanisms, including Transcription Termination Factor 2 (TTF2)-mediated removal of nascent transcripts, reinforce transcriptional shutdown. How these layers of regulation control individual RNA polymerases and influence transcriptional reactivation at mitotic exit remains poorly understood. Here, we probed how TTF2 differentially controls transcription of distinct RNA classes, using polymerase-specific perturbations and nascent RNA labelling across mitosis. Loss of TTF2 led to accumulation of chromatin-associated transcripts during metaphase, predominantly RNA Polymerase II-derived, consistent with its established role in transcriptional clearance. More unexpectedly, TTF2 depletion caused premature RNA Polymerase I reactivation during anaphase, resulting in unscheduled rRNA synthesis and early recruitment of nucleolar proteins. These findings place TTF2 as a novel regulator of RNA Polymerase I reactivation at mitotic exit. Disruption of this control persists beyond mitosis, resulting in increased nucleolar fragmentation in interphase. Together, these findings reveal TTF2 as a conserved regulator that interfaces with multiple RNA polymerases through functionally distinct modes of control, coordinating both transcriptional shutdown and timely reactivation across mitosis.

cell biology↗

bioRxiv2026

Removal of nascent transcripts by TTF2 is required for efficient sister chromatid resolution in human cells.

During mitosis, chromosome assembly is accompanied by a global shutdown of transcription. However, how this transcriptional silencing contributes to mitotic fidelity and genome stability remains poorly understood. Here, we used depletion of Transcription Termination Factor 2 (TTF2) - a key factor in mitotic transcriptional inactivation - to investigate the impact of pervasive transcription on mitotic fidelity. TTF2 depletion causes accumulation of elongating transcripts on mitotic chromatin and multiple mitotic defects, including abnormal chromosome alignment, delayed progression, and impaired chromosome compaction. Notably, defects in sister chromatid resolution are particularly prominent, with DNA bridges as the major segregation error, increasing micronuclei formation. These defects are linked to altered chromatin organisation, including R-loops accumulation at mis-segregating DNA. Most anaphase defects are suppressed when transcription is chemically inhibited, establishing a causal link between transcription and the observed mitotic defects. Our findings reveal how abnormal retention of transcriptional activity on mitotic chromatin disrupts mitosis, with impaired sister chromatid resolution linking transcriptional dysregulation to genome instability.

cell biology↗

bioRxiv2025

SLFN11 restricts escape from telomere crisis to prevent alternative lengthening of telomeres

The tRNA nuclease SLFN11 is epigenetically silenced in [~]50% of treatment-naive tumours and is the strongest predictor of chemoresistance but why it is frequently inactivated in cancer is unknown. To acquire immortality, cancer cells can activate alternative lengthening of telomeres (ALT), typically accompanied by ATRX loss. Here, we implicate SLFN11 in sensing telomere replication stress, triggering eradication of ATRX deficient cells prior to ALT establishment. Whereas progressive telomere shortening of cells lacking telomerase and ATRX leads to telomere crisis and cell death, SLFN11 loss confers tolerance to PML-BLM dependent ALT intermediates, permitting emergence of ALT survivors. We propose that during tumorigenesis SLFN11 inactivation is selected as means to tolerate endogenous replication stress following telomere crisis, leading to the development of therapy resistant tumours before treatment.

molecular biology↗

bioRxiv2023

Novel gut probiotic engages microbiota for recovery and pathobiont clearance while preventing inflammation

The microbiota inhabiting the mammalian gut serves as a protective barrier against pathogen invasion through a mechanism known as colonization resistance. Antibiotic treatments can inadvertently disturb the gut microbiota, compromising colonization resistance and increasing hosts susceptible to infections. Non-pneumoniae Klebsiella spp. members of the gut microbiota play a crucial role in colonization resistance and clearance from the gut of pathogenic Enterobacteriaceae following antibiotic-induced perturbations. Specifically, Klebsiella strain ARO112 a gut microbiota isolate, can effectively resist and clear Escherichia coli colonization after antibiotic-induced dysbiosis. We assessed the potential of Klebsiella sp ARO112 to promote clearance of Enterobacteriaceae pathobiont Adherent-Invasive E. coli (AIEC) in an Inflammatory Bowel Disease (IBD) mouse model susceptible to inflammatory episodes. In antibiotic-treated IBD-predisposed mice infected with the AIEC, Klebsiella sp. ARO112 promoted a faster recovery of gut microbiota members potentially involved in butyrate production and accelerated pathobiont clearance. Functionally, ARO112-driven microbiota recovery promoted higher butyrate levels and prevented intestinal inflammation compared to untreated animals. Conversely, treatment with the well-known probiotic E. coli Nissle 1917 enhanced AIEC colonization and inflammation. Furthermore, we assessed the safety of ARO112 as a potential next-generation probiotic; phenotypic comparison of ARO112 against closely related Enterobacteriaceae revealed its lower pathogenic potential, including being more recalcitrant to antibiotic resistance acquisition. Overall, our results showing that Klebsiella sp. ARO112 can resolve infections while contributing to the promotion of intestinal health, underscore its potential as a biotherapy agent that can disrupt inflammation-treatment-infection cycles. This potential extends beyond IBD patients, encompassing individuals with other inflammatory-based conditions related to microbiota imbalances.

microbiology↗

bioRxiv2023

Pervasive relaxed selection on spermatogenesis genes coincident with the evolution of polygyny in gorillas

Gorillas have a polygynous social system in which the highest-ranking male has almost exclusive access to females and sires most of the offspring in the troop. Such behavior results in a dramatic reduction of sperm competition, which is ultimately associated with numerous traits that cause low efficacy of gorilla spermatogenesis. However, the molecular basis behind the remarkable erosion of the gorilla male reproductive system remains unknown. Here, we explored the genetic implications of the polygynous social system in gorillas by testing for altered selection intensity across 13,310 orthologous protein-coding genes from 261 Eutherian mammals. We identified 578 genes with relaxed purifying selection in the gorilla lineage, compared with only 96 that were positively selected. Genes under relaxed purifying selection in gorillas have accumulated numerous deleterious amino acid substitutions, their expression is biased towards male germ cells and are enriched in functions related to meiosis and sperm biology. We tested the role of gorilla relaxed genes previously not implicated in male reproductive function using the Drosophila model system and identified 41 novel spermatogenesis genes required for normal fertility. Furthermore, by exploring exome/genome sequencing data of infertile men with severe spermatogenic impairment, we found that the human orthologs of the gorilla relaxed genes are enriched for loss-of-function variants in infertile men. These data provide compelling evidence that reduced sperm competition in gorillas is associated with relaxed purifying selection on genes related to male reproductive function. The accumulation of deleterious mutations in these genes likely provides the mechanistic basis behind the low efficacy of gorilla spermatogenesis and uncovers new candidate genes for human male infertility.

evolutionary biology↗

bioRxiv2022

An SNF2 helicase-like protein links mitotic transcription termination to sister chromatid resolution

AO_SCPLOWBSTRACTC_SCPLOWMitotic chromatin is largely assumed incompatible with transcription due to changes in the transcription machinery and chromosome architecture. However, the mechanisms of mitotic transcriptional inactivation and their interplay with chromosome assembly remain largely unknown. By monitoring ongoing transcription in Drosophila early embryos, we reveal that eviction of nascent mRNAs from mitotic chromatin occurs after substantial chromosome compaction and is not promoted by condensin I. Instead, we show that the timely removal of transcripts from mitotic chromatin is driven by the SNF2 helicase-like protein Lodestar (Lds), identified here as a modulator of sister chromatid cohesion defects. In addition to transcriptional termination, we uncovered that Lds cooperates with Topoisomerase 2 to ensure efficient sister chromatid resolution and mitotic fidelity. We conclude that mitotic transcriptional termination is not a passive consequence of cell cycle progression and/or chromosome compaction but occurs via dedicated mechanisms with functional parallelisms to sister chromatid resolution.

cell biology↗

bioRxiv2022

Endoplasmic Reticulum membranes are continuously required to maintain mitotic spindle size and forces

Membrane organelle function, localization, and proper partitioning upon cell division depend on interactions with the cytoskeleton. Whether, reciprocally, membrane organelles also impact on the function of cytoskeletal elements remains less clear. Here, we show that acute disruption of the Endoplasmic Reticulum (ER) around spindle poles affects mitotic spindle size and function in Drosophila syncytial embryos. Acute ER disruption was achieved through the inhibition of ER membrane fusion by the dominant-negative cytoplasmic domain of Atlastin. We reveal that when the ER is disrupted specifically at metaphase, mitotic spindles become smaller, despite no significant changes in microtubule dynamics. These smaller spindles are still able to mediate sister chromatid separation, yet with decreased velocity. Furthermore, by inducing mitotic exit, we found that nuclear separation and distribution are affected upon ER disruption. Our results suggest that ER integrity around spindle poles is crucial for the maintenance of mitotic spindle shape and pulling forces. Additionally, ER integrity also ensures nuclear spacing during syncytial divisions.

cell biology↗

bioRxiv2022

Condensin II is required for efficient Spindle Assembly Checkpoint activation in Drosophila male meiosis

Reductional nuclear division in meiosis is essential for diploid life. A fundamental event in meiosis is chromatin condensation, through mechanisms not yet fully understood. Current data suggest that Condensins are key players in building and sustaining mitotic and meiotic chromosome structure. In Drosophila, Condensin II appears to be dispensable for faithful mitosis in somatic tissues yet essential in the germline. Previous work has demonstrated that in Drosophila male meiosis, Condensin II is required for the segregation of homologous chromosomes into distinct territories during prophase I, possibly through the resolution of chromosomal intertwines. Here we show that in addition to this well-established function in meiotic chromatin assembly, Condensin II is required for robust Spindle Assembly Checkpoint (SAC) signaling in male meiosis. In the absence of Condensin II, spermatocytes undergo faster meiotic divisions and display reduced ability to prolong meiosis in the presence of spindle poisons. This is attributed to the inability to recruit a key SAC component (Mad1) to the kinetochore. Importantly, we demonstrate that the absence of a robust SAC response in Condensin II mutants, and consequent accelerated meiosis, is a strong contributor to the meiotic defects associated with these mutants. We show that artificial prolongation of meiotic divisions, using conditions that delay anaphase onset in a SAC-independent manner, is sufficient to rescue segregation defects and aneuploidy associated with Condensin II mutations. We therefore conclude that Condensin II can be dispensable for the resolution of topological problems and chromosome condensation if cells are able to prolong meiosis. Yet, the newly found role of this complex in the robustness of the SAC reduces meiotic timing leading to severe chromosome segregation defects.

cell biology↗

bioRxiv2021

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells

During mitosis, chromatin condensation is accompanied by a global arrest of transcription. Recent studies suggest transcriptional reactivation upon mitotic exit occurs in temporally coordinated waves, but the underlying regulatory principles have yet to be elucidated. In particular, the contribution of sequence-specific transcription factors (TFs) remains poorly understood. Here we report that Brn2, an important regulator of neural stem cell identity, associates with condensed chromatin throughout cell division, as assessed by live-cell imaging of proliferating neural stem cells. By contrast, the neuronal fate determinant Ascl1 dissociates from mitotic chromosomes. ChIP-seq analysis reveals that Brn2 mitotic-chromosome binding does not result in sequence-specific interactions prior to mitotic exit, relying mostly on electrostatic forces. Nevertheless, surveying active transcription using single-molecule RNA-FISH against immature transcripts, indicates the differential presence of TF near chromatin when exiting mitosis is associated with early (anaphase) versus late (early G1) reactivation of key targets of Brn2 and Ascl1, respectively. Moreover, by using a mitotic-specific dominant negative approach, we show that competing with Brn2 binding during mitotic exit reduces the transcription of its target gene Nestin. Our study shows an important role for differential binding of TFs to mitotic chromosomes, governed by their electrostatic properties, in defining the temporal order of transcriptional reactivation during mitosis-to-G1 transition.

developmental biology↗

bioRxiv2019

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs

That antibiotics alter microbiota composition and increase infection susceptibility is well known, but their generalizable effects on the gut commensal community and dependence on environmental variables remain open questions. Here, we systematically compared antibiotic responses in gnotobiotic and conventional mice across antibiotics, microbiotas, diets, and housing status. We identify remarkable resilience, whereby a humanized microbiota recovers before drug administration ends, with transient dominance of resistant Bacteroides and taxa-asymmetric reduction in diversity. In other cases, in vitro sensitivities were not predictive of in vivo responses, underscoring the significance of host and community contexts. A fiber-deficient diet exacerbated collapse of the microbiota and delayed recovery, despite the presence of a similar core community across diets at the point of maximal disturbance. Resilience to a second ciprofloxacin treatment was observed via response reprogramming, in which species replacement after ciprofloxacin treatment established resilience to a second treatment, and also through cross housing transmission. Single-housing drastically disrupted recovery, highlighting the importance of environmental microbial reservoirs and suggesting sanitation may exacerbate the duration of antibiotic-mediated disruption. Our findings highlight the ability of the commensal microbiota to deterministically adapt to large perturbations, and the translational potential for modulating diet, sanitation, and microbiota composition during antibiotics.

microbiology↗

bioRxiv2018

Delayed aneuploidy stress response of neural stem cells impairs adult lifespan in flies

SummaryStudying aneuploidy during organism development has strong limitations, as chronic mitotic perturbations used to generate aneuploidy result in lethality. We developed a genetic tool to induce aneuploidy in an acute and time controlled manner during Drosophila development. This is achieved by reversible depletion of cohesin, a key molecule controlling mitotic fidelity.\n\nLarvae challenged with aneuploidy hatch into adults with severe motor defects shortening their lifespan. Neural stem cells, despite being aneuploid, display a delayed stress response and continue proliferating, resulting in the rapid appearance of chromosomal instability, complex array of karyotypes and cellular abnormalities. Notably, when other brain cell-lineages are forced to self-renew, aneuploidy-associated stress response is significantly delayed, indicating that stemness state confers resistance to aneuploidy. Sparing solely the developing brain from induced aneuploidy is sufficient to rescue motor defects and adult lifespan, suggesting that neural tissue is the most ill-equipped to deal with developmental aneuploidy.\n\nHighlightsO_LIReversible depletion of cohesin results in just a round or two of aberrant cell divisions, generating high levels of aneuploidy.\nC_LIO_LILarvae challenged with aneuploidy during development hatch into impaired adults.\nC_LIO_LIFew cell cycles are sufficient for chromosomal instability to emerge from a previously stable aneuploid state.\nC_LIO_LINeural stemness delays aneuploidy stress response.\nC_LIO_LIProtecting only the neural tissue from aneuploidy rescues adult abnormalities and lifespan.\nC_LI

developmental biology↗

bioRxiv2018

Absence of the Spindle Assembly Checkpoint restores mitotic fidelity upon loss of sister chromatid cohesion

Sister chromatid cohesion is essential for faithful mitosis, as premature cohesion loss leads to random chromosome segregation and aneuploidy, resulting in abnormal development. To identify specific conditions capable of restoring defects associated with cohesion loss, we screened for genes whose depletion modulates Drosophila wing development when sister chromatid cohesion is impaired. Cohesion deficiency was induced by knock-down of the acetyltransferase Separation anxiety (San)/Naa50, a cohesin complex stabilizer. Several genes whose function impacts wing development upon cohesion loss were identified. Surprisingly, knockdown of key Spindle Assembly Checkpoint (SAC) proteins, Mad2 and Mps1, suppressed developmental defects associated with San depletion. SAC impairment upon cohesin removal, triggered by San depletion or artificial removal of the cohesin complex, prevented extensive genome shuffling, reduced segregation defects and restored cell survival. This counterintuitive phenotypic suppression was caused by an intrinsic bias for efficient chromosome bi-orientation at mitotic entry, coupled with slow engagement of error-correction reactions. We conclude that mitotic timing determines the severity of defects associated with cohesion deficiency. Therefore, although divisions are still error-prone, SAC inactivation enhances cell survival and tissue homeostasis upon cohesion loss.

cell biology↗