Biology subjects

Munoz-Canoves, P.

Publications and source records attributed to Munoz-Canoves, P..

10 recordsLinked to original sources

bioRxiv2026

Targeted ATAC-see (tATAC-see): A Visual Assay for Target-Specific Chromatin Profiling

We present targeted ATAC-see (tATAC-see), a visual genomics assay for site-specific chromatin profiling. By integrating the in situ visualization of ATAC-see with antibody-tethered tagmentation, tATAC-see captures chromatin states at defined protein-occupied domains with the simplicity of standard immunofluorescence. Modulating the spatial interaction radius of Tn5 via salt titration enables extended tagmentation of local chromatin environments near the target. We validated this imaging-based method by capturing the expanded chromatin neighborhoods of active euchromatin (H3K27ac, H3K4me3) alongside the dense structural lamina-associated domains (LADs) of lamin A/C and lamin B1. Using an HDAC inhibitor, we tested the assays sensitivity to detect dynamic structural remodeling. We not only tracked chromatin decompaction but also demonstrated the robust structural resistance of LADs. As a proof-of-principle biological application, we applied tATAC-see to models of replicative, chronological, and pathological (Hutchinson-Gilford progeria syndrome) aging to assess its ability to detect well-characterized peripheral heterochromatin and LAD remodeling. We observed divergent chromatin trajectories at the nuclear envelope, reflective of the lamins distinct roles. lamin B1 domains exhibit increased local accessibility consistent with age-associated heterochromatin erosion, while lamin A/C-associated domains physically detach from their scaffold. Ultimately, tATAC-see provides a robust, accessible platform for mechanistic and population-level studies to uncover spatial epigenome dynamics. Summary StatementtATAC-see is a tunable visual genomics assay that can capture target-specific chromatin remodeling across diverse biological contexts.

cell biology↗

bioRxiv2025

Titin cleavage is a driver of cardiomyocyte disengagement and reactive myocardial fibrosis

Myocardial remodeling including cardiomyocyte-death-independent, reactive fibrosis and disconnection of cardiomyocytes is at the basis of prevalent cardiac conditions converging into arrhythmias and heart failure. However, the molecular mechanisms behind these pathogenic responses remain incompletely understood limiting therapeutic opportunities. Here, we find that a molecular event common to unrelated heart diseases, namely the cleavage of the sarcomeric protein titin, is enough to trigger fast myocardial remodeling. Using an engineered system based on the expression of tobacco etch virus protease (TEVp) in mice, we show that 30% mosaic cardiac titin cleavage leads to global cardiomyocyte disengagement, activation of cardiac fibroblasts and interstitial collagen deposition. These effects are concurrent, involve ERK1/2 signaling, and are expected to contribute, at least, to myocardial remodeling in chemotherapy-induced cardiotoxicity and ischemia damage.

physiology↗

bioRxiv2025

The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function

Circadian clocks present throughout the brain and body coordinate diverse physiological processes to support daily homeostasis and respond to changing environmental conditions. The local dependencies within the mammalian clock network are not well defined. We previously demonstrated that the skeletal muscle clock controls transcript oscillations of genes involved in fatty acid metabolism in the liver, yet whether the liver clock also regulates the muscle was unknown. Here, we use hepatocyte-specific Bmal1 KO mice (Bmal1hep-/-) and reveal that approximately one third of transcriptional rhythms in skeletal muscle are regulated by the liver clock vivo. Treatment of myotubes with serum harvested from Bmal1hep-/- mice inhibited expression of genes involved in metabolic pathways, including oxidative phosphorylation. Overall, the transcriptional changes induced by liver clock-driven endocrine-communication revealed from our in vitro system were small in magnitude, leading us to surmise that the liver clock acts to fine-tune metabolic gene expression in muscle. Strikingly, treatment of myotubes with serum from Bmal1hep-/- mice inhibited mitochondrial ATP production compared to WT and this effect was only observed with serum harvested during the active phase. Overall, our results reveal communication between the liver clock and skeletal muscle-uncovering a bidirectional endocrine communication pathway dependent on clocks in these two key metabolic tissues. Targeting liver and muscle circadian clocks may represent a potential avenue for exploration for diseases associated with dysregulation of metabolism in these tissues.

cell biology↗

bioRxiv2025

The central clock drives metabolic rhythms in muscle stem cells

Circadian rhythms are essential for organismal health. Satellite cells (SCs), the muscle resident stem cells, maintain a state of quiescence yet exhibit robust circadian oscillations at the transcriptional level. Although peripheral clocks have been extensively studied in various tissues, how the intrinsic clock of stem cells interacts with the central, distal clock is largely unknown. We used SC-specific reconstitution of the essential clock gene Bmal1 to elucidate the role of the local SC clock and its interplay with the central clock in the mouse brain and found that daily transcriptional control of metabolic processes in SCs depend on central clock input, independent of the SC clock. Central clock-driven genes were involved in lipid metabolism, functionally important for SC-mediated muscle repair, and autophagy was required for their oscillation. In summary, we provide the first evidence of circadian coordination of central and local clocks for control of rhythmic gene expression in quiescent stem cells. HighlightsO_LIBrain:satellite cell clock communication restores rhythms of core clock machinery in quiescent satellite cells C_LIO_LIBrain inputs are the dominant regulator of transcript rhythms in SCs, driving the oscillation of lipid metabolic genes. C_LIO_LIAutophagy in satellite cells is required for the oscillation of lipid metabolic genes. C_LIO_LIEarly phases of muscle regeneration depend on brain-driven circadian signals. C_LI

cell biology↗

bioRxiv2024

Network-community analysis of cellular senescence

Most cellular phenotypes are genetically complex. Identifying the set of genes that are most closely associated with a specific cellular state is still an open question in many cases. Here we study the transcriptional profile of cellular senescence using a combination of network-based approaches, which include eigenvector centrality feature selection and community detection. We apply our method to cell-type-resolved RNA sequencing data obtained from injured muscle tissue in mice. The analysis identifies some genetic markers consistent with previous findings, and other previously unidentified ones, which are validated with previously published single-cell RNA sequencing data in a different type of tissue. The key identified genes, both those previously known and the newly identified ones, are transcriptional targets of factors known to be associated with established hallmarks of senescence, and can thus be interpreted as molecular correlates of such hallmarks. The method proposed here could be applied to any complex cellular phenotype even when only bulk RNA sequencing is available, provided the data is resolved by cell type.

systems biology↗

bioRxiv2023

Impact of Bmal1 rescue and time-restricted feeding on liver and muscle proteomes during the active phase in mice

ObjectiveMolecular clocks and daily feeding cycles support metabolism in peripheral tissues. Although the roles of local clocks and feeding is well defined at the transcriptional level, their impact on governing protein abundances in peripheral tissues is unclear. Here, we determine the relative contributions of the local molecular clock and daily feeding cycles on liver and muscle proteomes during feeding. MethodsLC-MS/MS was performed on liver and skeletal muscle harvested four hours into the dark phase from wild-type (WT), Bmal1 knockout (KO), and liver- and muscle-Bmal1-rescued (LMRE) mice housed under 12-h light/12-h dark cycles with either ad libitum feeding or nighttime-restricted feeding. Additional molecular and metabolic analyses were performed on liver and cultured hepatocytes. ResultsFeeding-fasting cycles had only minimal effects on liver and none on muscle. In contrast, Bmal1 KO altered the abundance of 674 proteins in liver, and 80 in muscle. Rescue of liver and muscle Bmal1 restored 50% of proteins in liver and 25% in muscle. These included proteins involved in carbohydrate metabolism in muscle and in fatty acid oxidation in liver. For liver, proteins involved in de novo lipogenesis were largely dependent on Bmal1 function in other tissues (i.e., the wider clock system). Proteins regulated by BMAL1 were enriched for secreted proteins; we determined that the maintenance of FGF1 abundance requires liver BMAL1, and that autocrine signaling through FGF1 is necessary and sufficient for mitochondrial respiration in hepatocytes. ConclusionsBMAL1 in liver and muscle is a more potent regulator of dark phase proteomes than daily feeding cycles, highlighting the need to assess protein levels in addition to mRNA when investigating clock mechanisms. The proteome is more extensively regulated by BMAL1 in liver than in muscle, and numerous metabolic pathways in peripheral tissues are reliant on the function of the clock system as a whole.

systems biology↗

bioRxiv2022

Interrogating Metabolic Interactions Between Skeletal Muscle and Liver Circadian Clocks In Vivo

Expressed throughout the body, the circadian clock system achieves daily metabolic homeostasis at every level of physiology, with clock disruption associated with metabolic disease (1, 2). Molecular clocks present in the brain, liver, adipose, pancreas and skeletal muscle each contribute to glucose homeostasis (3). However, it is unclear; 1) which organ clocks provide the most essential contributions, and 2) if these contributions depend on inter-organ communication. We recently showed that the liver clock alone is insufficient for most aspects of daily liver glucose handling and requires connections with other clocks (4). Considering the pathways that link glucose metabolism between liver and skeletal muscle, we sought to test whether a clock connection along this axis is important. Using our previous published methodology for tissue-specific rescue of Bmal1 in vivo (4, 5), we now show that in the absence of feeding-fasting cycles, liver and muscle clocks are not sufficient for systemic glucose metabolism, nor do they form a functional connection influencing local glucose handling or daily transcriptional rhythms in each tissue. However, the introduction of a daily feeding-fasting rhythm enables a synergistic state between liver and muscle clocks that leads to restoration of systemic glucose tolerance. These findings reveal limited autonomous capabilities of liver and muscle clocks and highlight the need for inter-organ clock communication for glucose homeostasis which involves at least two peripheral metabolic organs.

cell biology↗

bioRxiv2021

Large field of view-spatially resolved transcriptomics at nanoscale resolution

Spatially resolved transcriptomic technologies are promising tools to study cell fate decisions in a physical microenvironment, which is fundamental for enhancing our knowledge of mammalian development. However, the imbalance between resolution, transcript capture and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation mammalian embryos. Here, we combined DNA nanoball (DNB) patterned arrays and tissue RNA capture to create SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq). This approach allows transcriptomic profiling of large histological sections with high resolution and sensitivity. We have applied Stereo-seq to study the kinetics and directionality of transcriptional variation in a time course of mouse organogenesis. We used this information to gain insight into the molecular basis of regional specification, neuronal migration and differentiation in the developing brain. Furthermore, we mapped the expression of a panel of developmental disease-related loci on our global transcriptomic maps to define the spatiotemporal windows of tissue vulnerability. Our panoramic atlas constitutes an essential resource to investigate longstanding questions concerning normal and abnormal mammalian development.

cell biology↗

bioRxiv2020

mRNA translation control by Dhx36 binding to 5' UTR G-quadruplex structures is essential for skeletal muscle stem cell regenerative functions

Skeletal muscle has a remarkable ability to regenerate owing to its resident stem cells, also called satellite cells (SCs), that are normally quiescent. When stimulated by damage, SCs activate and expand to form new fibers. The mechanisms underlying SC proliferative progression remain poorly understood. Here we show that Dhx36, a helicase that unwinds RNA quadruplex (rG4) structures, is essential for muscle regeneration by regulating SC expansion. We find that Dhx36 (initially named RHAU) is barely expressed at quiescence and is highly induced during SC activation and proliferation. Inducible deletion of Dhx36 in adult SCs causes defective proliferation and muscle regeneration after damage. System-wide mapping in proliferating SCs revealed Dhx36 binding predominantly to rG4 structures at various regions of mRNAs, while integrated polysome profiling showed that Dhx36 promotes mRNA translation via 5UTR rG4 binding. Furthermore, we demonstrate that Dhx36 specifically regulates the translation of Gnai2 mRNA by unwinding its 5UTR rG4 structures and identify Gnai2 as a downstream effector of Dhx36 for SC expansion. Altogether our findings uncover Dhx36 as an indispensable post-transcriptional regulator of SC function and muscle regeneration through binding and unwinding rG4 structures at 5UTR of target mRNAs.

cell biology↗

bioRxiv2020

In-vivo Transcriptomic Profiling of Systemic Aging using Cell Encapsulation

Sustained exposure to a young systemic environment rejuvenates aged organisms and promotes cellular function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint niche-independent effects of circulating factors on specific cell populations. Here we describe a method for the encapsulation of human and mouse skeletal muscle progenitors in diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic aging in vivo independent of heterogeneous short-range tissue interactions. We observed that circulating long-range signaling factors in the old systemic environment lead to an activation of Myc and E2F transcription factors, induce senescence and suppress myogenic differentiation. Importantly, in vitro profiling using young and old serum in 2D culture does not capture all pathways deregulated in encapsulated cells in aged mice. Thus, in vivo transcriptomic profiling using cell encapsulation allows for the characterization of effector pathways of systemic aging with unparalleled accuracy.

bioengineering↗