Biology subjects

Cavallaro, M.

Publications and source records attributed to Cavallaro, M..

7 recordsLinked to original sources

bioRxiv2026

Linking H3K36me3 to transcriptional dynamics

Genes are transcribed in bursts as they fluctuate between on and off states, in a process modulated by histone modifications. The mammalian histone methyltransferase SETD2 is solely responsible for depositing H3K36 trimethylation, which recruits histone deacetylases and regulates histone occupancy. Nucleosomes are known to act as a barrier to transcription elongation and have been observed to impact elongation rate. H3K36me3 has been associated with long pausing sites in gene bodies and is implicated in reducing speed of successive RNA polymerase II. However, the role of SETD2 and H3K36me3 in transcriptional dynamics are unknown. Here we show upon SETD2 knockout and H3K36me3 depletion in murine C2C12 myoblast cells that overall gene expression is reduced and splicing fidelity affected, as 5' mutually exclusive exons are favoured over 3' ones. Furthermore, transcriptional burst size is reduced, while bursting frequency increased. A simple mathematical model suggests that the observed changes in transcriptional dynamics can be explained by less stringently controlled polymerase pausing in the gene bodies of H3K36me3 depleted cells.

systems biology↗

bioRxiv2026

Vegfr3 is required in the Tbx1 expression domain for cardiac outflow tract development.

Gene inactivation in model organisms has identified numerous genes and signaling pathways involved in mammalian cardiac OFT development. Human genetics data have implicated the VEGFR3 gene in OFT development but when and where it is required is unknown. In this study we determined the sensitivity of the developing murine cardiac OFT to reduced Vegfr3 gene dosage and we tested whether its requirement is dependent upon TBX1, a known regulator of Vegfr3 expression in cardiac and lymphatic endothelial cells. We found that in the mouse, a single copy if the Vegfr3 gene was sufficient for normal cardiac OFT development in most cases. Mutation of a single copy of the Tbx1 gene greatly enhanced the sensitivity of OFT development to Vegfr3 dosage reduction and led to the formation of severe OFT anomalies. In addition, deletion of Vegfr3 in the Tbx1 expression domain also led to OFT abnormalities. We used RNAscope to reveal the location of Vegfr3 and Tbx1 transcripts in midterm mouse embryos. This revealed co-localization of these transcripts that was restricted to the aortic sac endothelium, suggesting that the distal OFT is a potential site of genetic interaction between Vegfr3 and TBX1 that is critical for normal OFT development.

developmental biology↗

bioRxiv2026

How many phage species remain undiscovered? Species sampling approaches to inform phage discovery

The emergence of antimicrobial resistant bacteria has been identified as one of the most serious public health and development threats for the near future. The use of bacteriophages (phages) is a promising solution for the sustainable control of these pathogens. Phages are natural viral predators of bacterial pathogens. However, due to the variability and adaptability of bacteria, developing effective and sustainable phage treatments requires drawing from a wide variety of different phage species. This study applies specialised mathematical and computational estimation approaches to the problem of sampling and discovering species of phages in microbiological communities. Our goal is to predict how many new phage species will be discovered in future samples based on species recorded in a phage sequence database for eight common bacterial hosts. While internal validation shows that current estimators yield low prediction errors for how many new species can be found when sampling more phages, these critically assume that the underlying mechanisms of phage sampling and database inclusion remain similar across time - an assumption put into question by our analysis for all but the host genus Mycobacterium. From this, we discuss how our results can still inform future sampling strategies - both through directly predicting the number of additional species, or by detecting changes in sampling and database inclusion. Our results have the potential to inform and optimise the hunt for and isolation of novel of phages from the the natural environment. HighlightsO_LISpecies abundance distribution of phages infecting seven of eight analysed host bacterial genera collected in phage databases changed significantly over time. C_LIO_LIMaintaining current sampling strategies for phages of host Mycobacteriut may lead to diminishing returns in the number of new phages found in additional samples. C_LIO_LIBoth non-parametric and parametric estimators of the numbers of unseen species show comparable, moderate errors when predicting a random subset from the remainder of hostspecific phage sets from the INPHARED database C_LI

genomics↗

bioRxiv2025

A multivalent mRNA-LNP therapeutic vaccine with broad cross-genotype immunogenicity elicits clearance of HBV infected hepatocytes

Chronic hepatitis B remains a major global health challenge, affecting over 254 million individuals and causing over 1 million deaths annually. Despite current antiviral therapies effectively suppressing viral replication, functional cure rates are low due to HBV-induced immune dysfunction and exhaustion. Therefore, new therapeutic approaches to achieve immune control of HBV infection are needed. Following the systematic evaluation of multiple HBV mRNA antigen designs, we developed mRNA-1965, a trivalent therapeutic mRNA vaccine encoding nanoparticle-displayed PreS1 and PreS2 domains of HBsAg to bypass the immune interference caused by HBV subviral particles, along with mutant forms of HBV Core and Polymerase. In HBV naive mice, mRNA-1965 immunization induced dose-dependent HBV-neutralizing antibodies and Th1-skewed CD4+ and IFN{gamma}+ CD8+ T cell responses to all three encoded HBV antigens. In non-human primates, mRNA-1965 elicited broad antibody and T cell responses across multiple HBV genotypes. Furthermore, vaccination with mRNA-1965 achieved a strong neutralizing antibody response and complete clearance of serum and liver HBV biomarkers in in an AAV-HBV mouse model with [~]100 IU/mL baseline HBsAg. Notably, combining mRNA-1965 with immune stimulatory co-modalities targeting PD-L1 and OX40 further enhanced therapeutic efficacy in mice with [~]1000 IU/mL baseline HBsAg. Clearance of HBV in AAV-HBV mice was associated with T cell response to mRNA-encoded antigens and with activation and differentiation of Core-specific CD8+ T cells. These findings support the potential of mRNA-1965 to promote a functional cure for chronic hepatitis B by overcoming immune dysfunction and subsequently enabling robust, functional immunity.

immunology↗

bioRxiv2021

SARS-CoV-2 Spike Affinity and Dynamics Exclude the Strict Requirement of an Intermediate Host

SARS-CoV-2 proximal origin is still unclear, limiting the possibility of foreseeing other spillover events with pandemic potential. Here we propose an evolutionary model based on the thorough dissection of SARS-CoV-2 and RaTG13 - the closest bat relative - spike dynamics, kinetics and binding to ACE2. Our results indicate that both spikes share nearly identical, high affinities for Rhinolophus affinis bat and human ACE2, pointing out to negligible species barriers directly related to receptor binding. Also, SARS-CoV-2 spike shows a higher degree of dynamics and kinetics optimization that favors ACE2 engagement. Therefore, we devise an affinity-independent evolutionary process that likely took place in R. affinis bats and limits the eventual involvement of other animal species in initiating the pandemic to the role of vector.

microbiology↗

bioRxiv2019

Polymerase recycling contributes to transcriptional noise

BackgroundTranscription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3 and 5 ends of a gene that enable reinitiation of transcription upon termination. ResultsUsing Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment. ConclusionsInteractions between the 3 and 5 ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.

systems biology↗

bioRxiv2018

Timing Polymerase Pausing with TV-PRO-seq

Transcription of many genes in metazoans is subject to polymerase pausing, which is the transient stop of transcriptionally-engaged polymerases. This is known to mainly occur in promoter proximal regions but it is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking. We present here the time-variant precision nuclear run-on and sequencing (TV-PRO-seq) assay, an extension of the standard PRO-seq that allows us to estimate genome-wide pausing times at single-base resolution. Its application to human cells demonstrates that, proximal to promoters, polymerases pause more frequently but for shorter times than in other genomic regions. Pausing release by the detergent sarkosyl, previously believed to be linked to the factor NELF at the promoter proximal region only, is independent of the latter. Comparison with single-cell gene expression data reveals that the polymerase pausing times are longer in highly expressed genes, while transcriptionally noisier genes have higher pausing frequencies and slightly longer pausing times. Analyses of histone modifications suggest that the marker H3K36me3 is related to the polymerase pausing.

systems biology↗