Biology subjects

Martin, B.

Publications and source records attributed to Martin, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Voluntary wheel running selectively preserves skeletal muscle during pancreatic cancer cachexia despite persistent systemic alterations

Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is frequently associated with cancer cachexia, involving alterations across multiple physiological systems. Whether distinct exercise paradigms similarly influence these compartments remains unclear. We compared voluntary wheel running (VWR) and treadmill running (TR) using an integrative physiological approach in a murine model of pancreatic cancer cachexia. Methods Male C57BL/6J mice bearing UN-KC-6141 pancreatic tumor cells were allocated to inactive control (CaCTL), VWR or TR groups and compared with healthy controls. Tumor progression, body composition, skeletal muscle, adipose tissue, hepatic metabolism, systemic inflammation, energy expenditure and behavior were assessed. Analysis of covariance determined whether tissue-mass differences remained evident after adjustment for tumor burden. Results UN-KC-6141 tumors induced a systemic cachectic phenotype involving skeletal muscle and adipose tissue wasting, hepatic metabolic remodeling, systemic inflammation and behavioral alterations. VWR slowed tumor growth, reduced final tumor mass, improved the body-weight trajectory and preserved lean and skeletal muscle mass, whereas TR did not reproduce these adaptations. Greater gastrocnemius mass with VWR remained evident after adjustment for tumor mass, indicating that reduced tumor burden alone was insufficient to account for muscle preservation. In contrast, adipose tissue wasting, hepatic metabolic remodeling and systemic inflammation remained largely unaffected. TR was also associated with a less favorable body-weight trajectory and greater fat mass loss than in inactive tumor-bearing mice. Exploratory metabolic phenotyping revealed distinct feeding, sleep and resting energy expenditure patterns between the two exercise paradigms. Conclusions VWR selectively preserved skeletal muscle within a persistently altered systemic environment, whereas the TR protocol used here did not reproduce these adaptations. These findings reveal tissue-specific exercise responsiveness during pancreatic cancer cachexia and highlight exercise paradigm characteristics as determinants of tumor-host adaptation.

physiology↗

bioRxiv2026

Distinct iron metabolism regulation during cachexia progression in murine models of intestinal and pancreatic cancer

Background. Cancer cachexia is a multifactorial syndrome characterized by substantial metabolic disturbances including systemic inflammation, and muscle atrophy, which may affect the regulation of iron metabolism in patients. This study aimed to characterize this regulation in two murine models of colorectal and pancreatic cancer, both associated with a high prevalence of cachexia. Methods. Histological, biochemical and molecular analyses were performed in serum, skeletal muscle, liver, spleen and tumor from UN-KC-6141 pancreatic tumor bearing mice and from ApcMin/+ mice (colorectal cancer model), both models exhibiting variable cachexia severity. Results. Both models induce cachexia, but diverge markedly in their regulation of iron metabolism. UNKC mice display reduced plasma iron availability (-9.6% transferrin saturation, p<0.001) without concomitant anemia, while hepatic hepcidin synthesis is upregulated (+100.6%, p<0.001) by inflammation, promoting ferroportin (FPN) downregulation (-42.4%, p<0.001) and iron sequestration in the spleen (+134% total iron content, p<0.001). In the atrophied gastrocnemius, iron concentration is preserved through increased ferritin (+86.6%, p=0.010) and hemoproteins (i.e., myoglobin, CYSC, COXIV) expression. Conversely, ApcMin/+ mice exhibit anemia together with hepatic and splenic iron depletion (-48.4%, p<0.001 and -84.9%, p<0.001, respectively). Hepcidin synthesis is downregulated (-99.9%, p<0.001) despite persistent inflammation, indicating that hypoxia and/or iron-deficiency signals probably predominate over the inflammatory pathway. FPN is markedly decreased (-94.2%, p<0.001) in the iron-depleted spleen despite low hepcidin. In the atrophied quadriceps of ApcMin/+ mice, iron deficiency is associated with decreased FPN and ferritin (-87.9%, p<0.001, and -38.4%, p=0.016, respectively), and increased TfR1 expression (+305%, p=0.107). Finally, tumor iron import may play a significant role in cachexia progression, as suggested by the association between tumor weight, tumor TfR1 protein levels and body weight loss in UNKC mice. Conclusion. These findings reveal cancer type-specific signatures of iron regulation in cachexia, which appear to be more driven by cancer type specific features than by cachexia severity itself, with skeletal muscle iron metabolism impaired mainly when cachexia is associated with anemia. This suggests that the clinical management of iron metabolism in cachectic patients should be guided by the underlying cancer type.

physiology↗

bioRxiv2026

The CNS-penetrant MAP4K inhibitor famlasertib restrains medulloblastoma dissemination without developmental toxicity

Cerebellum tissue invasion and dissemination are major drivers of recurrence and metastatic spread in medulloblastoma (MB), yet no invasion-inhibitory therapy is currently available. The serine/threonine kinase MAP4K4 is highly expressed in MB and promotes invasive behavior downstream of growth factor signaling, while its physiological postnatal downregulation suggests that disrupted developmental control may contribute to tumor pathogenesis. Here, we investigate pharmacological targeting of MAP4K4 using famlasertib, a CNS-penetrant, neuroprotective MAP4K inhibitor, as a strategy to suppress invasion in MB. Using 3D invasion assays and quantitative live-cell microscopy, we demonstrate that famlasertib markedly reduces invasive behavior and single-cell motility of MB cells. Organotypic cerebellum tissue and orthotopically implanted zebrafish larval models further confirm anti-invasive efficacy without detectable developmental toxicity at effective concentrations. Phospho-proteomics and functional analyses revealed that MAP4K inhibition alters kinase signaling linked to cytoskeletal remodeling, leading to suppressed F-actin dynamics, increased cell clustering, and enhanced cortical accumulation of tight junction protein 1 (TJP1). Collectively, our findings confirm MAP4Ks as therapeutically targetable regulators of MB invasion and establish famlasertib as a candidate migrastatic agent that restrains tumor cell dissemination while preserving developmental integrity.

cancer biology↗

bioRxiv2026

A liquid handling platform for standardised quantification of cell-free enzymatic activity encoded by antimicrobial resistance genes

Antimicrobial resistance (AMR) is a growing global threat to human health, and rapid methods for characterising emerging antimicrobial resistance genes (ARGs) are needed. Here, we develop a semi-automated workflow using cell-free gene expression (CFE) systems to measure the activity of two ARGs encoded on plasmid DNA that produce rifampicin-inactivating and gentamicin-inactivating enzymes. We validated the use of a small benchtop Myra liquid handling system compared to manual pipetting, with no statistical differences observed. After optimising the pre-incubation time of ARGs and dispensing protocol, expression of aac(3)-IIa increased the half-maximal inhibition concentration (IC50) of gentamicin by over 150-fold, while arr-3 increased the IC50 of rifampicin by approximately 20-fold compared to controls. Future work could extend this platform to characterise novel ARGs identified through genomic surveillance or rapidly profile activity of new or derivative antibiotics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/720151v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@50bbdcorg.highwire.dtl.DTLVardef@5d98e4org.highwire.dtl.DTLVardef@e0a3fforg.highwire.dtl.DTLVardef@2ef12a_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2026

Reef fish escape responses selectively match predator attack speeds

Animals must continually balance foraging with the risk of predation. In complex natural environments, this means quickly distinguishing between threats and harmless situations. We investigated how site-associated coral reef fishes decide to escape in response to visual cues mimicking predator attacks, using controlled underwater presentations of looming stimuli at varying speeds. We measured escape responses across species and social contexts, comparing them to predator attack speeds observed in the same habitat. Escape responses were highly sensitive to the speed of the looming stimulus, with no responses occurring at low speeds. The speeds triggering escape matched those of predator attacks, whereas cruising swim speeds never triggered a response. Species employed distinct antipredator strategies: Brown Chromis foraged away from shelter with high responsiveness, whereas Bicolor Damselfish remained shelter-dependent with lower escape propensities. Contrary to expectations, the social factors did not affect responses in this study. These findings demonstrate that reef fish are highly sensitive to the approach speed of objects, with species-specific strategies further shaping behaviors. By combining realistic visual threats with natural predator attack data, this study offers insight into how animals make escape decisions in complex, real-world environments.

animal behavior and cognition↗

bioRxiv2026

Functional redundancy and anaerobic metabolism characterize the skin microbiome of a critically endangered sawfish

Using shotgun metagenomics of largetooth sawfish (Pristis pristis) skin and paired pool water samples, we provide the first taxonomic and functional characterization of a sawfish skin microbiome and assess its ecological distinctiveness, assembly, and resilience relative to the surrounding water column. The skin microbiome was strongly host-associated and compositionally distinct, with lower taxonomic richness than the water column but dominated by Bacillota, particularly spore-forming Bacilli. Functional profiling revealed enrichment of genes associated with sporulation, dormancy, anaerobic metabolism, and peptide transport, consistent with adaptation to low-oxygen, low-flow pool conditions. In contrast, water-column microbiomes were more taxonomically diverse and enriched in phototrophic and polysaccharide-utilization pathways. Despite reduced taxonomic diversity, sawfish skin communities exhibited higher functional redundancy, with gene functions accumulating more rapidly per taxon. This pattern supports a host-filtered, lottery-like assembly process that produces taxonomically variable yet functionally conserved communities. The enrichment of dormancy and anaerobic pathways suggests the skin microbiome persists through periods of host quiescence and environmental stress while maintaining metabolic potential. Together, these results demonstrate that the sawfish skin supports a resilient, functionally robust microbiome distinct from ambient aquatic communities, highlighting the potential for integrating microbial functional data into conservation strategies for Critically Endangered vertebrates.

ecology↗

bioRxiv2025

The Pioneer Transcription Factor Oct4 Differentially Co-opts Bcl11a and Bcl11b to Regulate Reprogramming to Pluripotency

Pioneer transcription factors (TFs) orchestrate development, reprogramming, and cancer. Yet, the molecular mechanisms by which they cooperate with endogenous TFs and chromatin to trigger cell fate conversions remain largely unknown. Here, we identified antagonistic functions in reprogramming to pluripotency for the two paralogous somatic zinc finger TFs Bcl11a and Bcl11b. We reveal that Bcl11a and Bcl11b are initially co-expressed in mouse embryonic fibroblasts and then segregate in cellular intermediates respectively prone or refractory to reprogramming, transdifferentiation, and oncogenic transformation. They exert opposite functions - with Bcl11a promoting and Bcl11b hindering - the efficacy of induced pluripotent stem cells generation. During reprogramming, we uncover that Bcl11b safeguards cellular identity by persistently binding to differentiation genes with Runx1 in refractory intermediates. In contrast, in reprogramming intermediates, Bcl11a interacts with Oct4 and is initially displaced from MEF enhancers. Bcl11a then binds transiently and contributes to activate the E3 ubiquitin ligase Pja1 that regulates Smad3, thus promoting mesenchymal-epithelial transition and constraining senescence. Collectively, our work unveils how the differential repurposing of paralogous TFs by Oct4 orchestrates reprogramming to pluripotency.

cell biology↗

bioRxiv2025

RealTrace: Uncovering biological dynamics hidden under measurement noise in time-lapse microscopy data

One of the most powerful approaches for identifying the mechanisms underlying complex biological phenomena is not just to measure bulk populations, or even take single-cell snapshots, but to directly track the behaviors of single cells in time. Indeed, in recent years there has been a steep rise in the use of time-lapse microscopy with fluorescent reporters to quantify single-cell time dynamics in many different biological systems. However, there is a major challenge with the analysis of such data. Since biological changes are inherently small on short time scales, much of the true biological dynamics is hidden under unavoidable measurement noise, but we do not know what functional form the time dynamics may take, and smoothing over neighboring time points simply replaces the true dynamics with a time average. Here, we present RealTrace, a Bayesian method that rigorously solves this challenge using only the assumption that, while true biological fluctuations are correlated on short time scales, measurement errors are uncorrelated. We show that this assumption can be formalized in a Bayesian model using maximum entropy process priors and that this model can be accurately solved by recursively approximating the non-linear dynamics over short time intervals. Given raw input cell size and fluorescence measurements, RealTrace calculates the estimated true sizes, total GFP contents, instantaneous growth rates, and volumic GFP production rates across all cells and time, together with rigorous error bars on all these quantities. We demonstrate the broad applicability of RealTrace by analyzing time-lapse microscopy datasets from E. coli bacteria, mouse embryonic stem cells, and entire C. elegans embryos. To exemplify the subtle dynamical features RealTrace can uncover, we perform an in-depth study of E. coli cells carrying fluorescent reporters for constitutive and ribosomal promoters, across multiple growth conditions. We find growth rates of single cells substantially fluctuate in time and, as the average growth rate decreases, these fluctuations systematically increase in amplitude and duration. Both growth rate and gene expression vary systematically across the cell cycle, but while the pattern of growth rate variation is condition-independent, the systematic variation in gene expression across the cell cycle is both condition and promoter-dependent. Finally, under a sudden change in nutrients, single cells exhibit highly consistent transient changes in growth rate and gene expression. While gene expression rates settle into a new steady-state surprisingly rapidly, the growth rate shows a dramatic drop followed by an overshoot that takes several cell cycles to settle down. All these observations give fundamental new insights into the single-cell physiology of bacteria. RealTrace is a highly versatile method that accurately removes measurement noise from any fluorescence time-lapse microscopy data, enabling the identification and quantification of subtle features in the biological dynamics that would otherwise be hidden under measurement noise.

bioinformatics↗

bioRxiv2025

A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms

Understanding biological systems requires observing features and processes across vast spatial and temporal scales, spanning nanometers to centimeters and milliseconds to days, often using multiple imaging modalities within complex native microenvironments. Yet, achieving this comprehensive view is challenging because microscopes optimized for specific tasks typically lack versatility due to inherent optical and sample handling trade-offs, and frequently suffer performance degradation from sample-induced optical aberrations in multicellular contexts. Here, we present MOSAIC, a reconfigurable microscope that integrates multiple advanced imaging techniques including light-sheet, label-free, super-resolution, and multi-photon, all equipped with adaptive optics. MOSAIC enables non-invasive imaging of subcellular dynamics in both cultured cells and live multicellular organisms, nanoscale mapping of molecular architectures across millimeter-scale expanded tissues, and structural/functional neural imaging within live mice. MOSAIC facilitates correlative studies across biological scales within the same specimen, providing an integrated platform for broad biological investigation.

cell biology↗

bioRxiv2024

Neuropeptide Dynamics Coordinate Layered Plasticity Mechanisms Adapting Drosophila Circadian Behavior to Changing Environment.

The Drosophila brain contains distinct sets of circadian oscillators responsible for generating the morning and evening bouts of locomotor activity, giving rise to a bimodal rest-activity pattern in light-dark cycles. We lack a mechanistic understanding of how environmental changes reshape this daily profile of rest-activity pattern. Here, we uncover a seasonal switch mechanism that remodels the evening bout of activity. Under summer-like conditions, an environment favored by fruit flies in temperate climates, levels of the PDF neuropeptide diminish, triggering a cascade. Lowered PDFR signaling disinhibits GSK3/SGG to advance the evening output. Upon sensing PDF loss, the neural activity weakens in the DN1p-SIFa circuit, responsible for promoting afternoon rest; leading to an earlier appearance of the evening peak. At the same time, the functional connections from DN1p to LNd oscillators strengthen, consequently handing over the evening pacemaker role to the DN1ps. Taken together, our findings elucidate how environment-induced changes in PDFR signaling tip the balanced output of the clock network, aligning daily rhythms with seasonal time. Neuropeptide-driven parallel adjustment of clock circuitry and clock protein functioning likely represents a conserved strategy across animal species, enabling them to adapt their daily behavior to seasonal changes throughout the year.

neuroscience↗

bioRxiv2024

HLA-E and NKG2A Mediate Resistance to M. bovis BCG Immunotherapy in Non-Muscle-Invasive Bladder Cancer

BackgroundBacillus Calmette-Guerin (BCG) is the standard of care treatment for high-risk non-muscle-invasive bladder cancer (NMIBC), yet many patients develop recurrent disease despite evidence of ongoing immune activation. We investigated mechanisms of immune escape in BCG-unresponsive tumors and evaluated the therapeutic potential of targeting the HLA-E/NKG2A axis. MethodsSingle-cell RNA sequencing, spatial immunophenotyping, proteomic profiling, and functional ex vivo assays were performed using tumors and urine samples from patients with BCG-naive and BCG-unresponsive NMIBC. ResultsBCG-unresponsive tumors were enriched for HLA-E-expressing malignant cells compared with BCG-naive tumors. Increased HLA-E expression was associated with enhanced IFN-{gamma} signaling and was induced by IFN-{gamma} stimulation in primary tumor cells and bladder cancer tumor lines. Spatial analyses demonstrated accumulation of NKG2A+ NK and CD8 T cells in proximity to HLA-Ehigh tumor cells, with increased NKG2A:HLA-E interactions in BCG-unresponsive tumors. Despite high expression of cytotoxic mediators, NKG2A+ effector cells displayed impaired degranulation. Blockade of NKG2A with monalizumab restored degranulation of and cytotoxicity by tumor-infiltrating lymphocytes in autologous tumor co-cultures. ConclusionsBCG-unresponsive NMIBC tumors are enriched for HLA-E-expressing tumor cells and NKG2A+ effector lymphocytes, with increased engagement of the HLA-E/NKG2A axis within the tumor microenvironment. These findings identify the HLA-E/NKG2A axis as a therapeutic vulnerability and provide a rationale for clinical evaluation of NKG2A blockade as a bladder-sparing strategy for patients with BCG-unresponsive disease.

cancer biology↗

bioRxiv2024

Coordination of protein synthesis and decay in mammalian cells

The maintenance of cellular homeostasis requires tight regulation of proteome concentration and composition. To achieve this, protein production and elimination must be robustly coordinated. However, the mechanistic basis of this coordination remains unclear. Here, we address this question using quantitative live cell imaging, computational modeling, transcriptomics, and proteomics approaches. We found that protein decay rates systematically adapt to global alterations of protein synthesis rates. This adaptation is driven by a core passive mechanism supplemented by facultative changes in mTOR signaling. Passive adaptation hinges on changes in the production rate of the machinery governing protein decay and allows partial maintenance of the cellular proteome. Sustained changes in mTOR signaling provide an additional layer of adaptation unique to naive pluripotent stem cells, allowing near-perfect maintenance of proteome composition. Our work unravels the mechanisms protecting the integrity of mammalian proteomes upon variations in protein synthesis rates.

cell biology↗

bioRxiv2024

Butyrate and propionate are microbial danger signals that activate the NLRP3-inflammasome in human macrophages in the presence of TLR stimulation

Short chain fatty acids (SCFAs) are immunomodulatory compounds produced by the microbiome through fermentation of dietary fibre. Although they are generally considered beneficial for gut health, patients suffering from inflammatory bowel disease (IBD) have shown poor tolerance to fibre-rich diets, suggesting that SCFAs may have contrary effects under inflammatory conditions. To investigate this, we examined the effect of SCFAs on human macrophages in the presence of toll-like receptor agonists. In contrast to their anti-inflammatory effects under steady state conditions, we observed that the SCFAs butyrate and propionate triggered the activation of the NLRP3 inflammasome when added in conjunction with TLR agonists. Mechanistically, butyrate and propionate activated NLRP3 by inhibiting HDACs 1-3 and 10, leading to an uneven distribution of histone hyperacetylation that resulted in alterations in the transcriptome. Specifically, there was a lack of hyperacetylation at the loci of the CFLAR and IL10 genes, two important inhibitors of NLRP3 inflammasome activation. The concurrent loss of transcription and protein expression of cFLIP and IL-10 enabled caspase-8-dependent NLRP3-inflammasome activation. SCFA-driven NLRP3 activation did not require potassium efflux and did not result in cell death but rather triggered hyperactivation and IL-1{beta} release. Our findings demonstrate that butyrate and propionate are bacterially-derived, viability-dependent danger signals (vita-PAMPs) that regulate NLRP3 inflammasome activation through epigenetic modulation of the inflammatory response. SummaryUnder inflammatory conditions, SCFAs are bacterially-derived, viability-dependent danger signals that, through HDAC inhibition and epigenetic modification, prevent expression of the anti-cell death gene cFLIP to trigger activation of the NLRP3 inflammasome.

immunology↗

bioRxiv2024

The effect of enriched versus inadequate housing conditions on eucalyptus smoke-induced cardiovascular dysfunction in mice

Living conditions play a major role in health and well-being, particularly for the cardiovascular and pulmonary systems. Depleted housing contributes to impairment and development of disease, but how it impacts body resiliency during exposure to environmental stressors is unknown. This study examined the effect of depleted (DH) versus enriched housing (EH) on cardiopulmonary function and subsequent responses to wildfire smoke. Two cohorts of healthy female mice, one of them surgically implanted with radiotelemeters for the measurement of electrocardiogram, body temperature (Tco) and activity, were housed in either DH or EH for 7 weeks. Telemetered mice were exposed for 1 hour to filtered air (FA) and then flaming eucalyptus wildfire smoke (WS) while untelemetered mice, which were used for ventilatory assessment and tissue collection, were exposed to either FA or WS. Animals were continuously monitored for 5-7 days after exposure. EH prevented a decrease in Tco after radiotelemetry surgery. EH mice also had significantly higher activity levels and lower heart rate during and after FA and WS. Moreover, EH caused a decreased number of cardiac arrhythmias during WS. WS caused ventilatory depression in DH mice but not EH mice. Housing enrichment also upregulated the expression of cardioprotective genes in the heart. The results of this study indicate that housing conditions impact overall health and cardiopulmonary function. More importantly, depleted housing appears to worsen the response to air pollution. Thus, non-chemical factors should be considered when assessing the susceptibility of populations, especially when it comes to extreme environmental events.

pharmacology and toxicology↗

bioRxiv2023

CZ CELLxGENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data

Hundreds of millions of single cells have been analyzed to date using high throughput transcriptomic methods, thanks to technological advances driving the increasingly rapid generation of single-cell data. This provides an exciting opportunity for unlocking new insights into health and disease, made possible by meta-analysis that span diverse datasets building on recent advances in large language models and other machine learning approaches. Despite the promise of these and emerging analytical tools for analyzing large amounts of data, a major challenge remains the sheer number of datasets and inconsistent format, data models and accessibility. Many datasets are available via unique portals platforms that often lack interoperability. Here, we present CZ CellxGene Discover (cellxgene.cziscience.com), a data platform that provides curated and interoperable data. This single-cell data resource, available via a free-to-use online data portal, hosts a growing corpus of community contributed data that spans more than 50 million unique cells. Curated, standardized, and associated with consistent cell-level metadata, this collection of interoperable single-cell transcriptomic data is the largest of its kind. A suite of tools and features enables accessibility and reusability of the data via both computational and visual interfaces to allow researchers to rapidly explore individual datasets and perform cross-corpus analysis. This functionality is enabling meta-analyses of tens of millions of cells across studies and tissues and providing global views of human cells at the resolution of single cells.

cell biology↗

bioRxiv2023

Unveiling the antiviral capabilities of targeting Human Dihydroorotate Dehydrogenase against SARS-CoV-2

The urgent need for effective treatments against emerging viral diseases, driven by drug-resistant strains and new viral variants, remains critical. We focus on inhibiting the human dihydroorotate dehydrogenase (HsDHODH), one of the enzymes in charge of pyrimidine nucleotide synthesis. This strategy could impede viral replication without provoking resistance. We evaluated quinone-based compounds, discovering potent HsDHODH inhibition (low nanomolar IC50) and promising in vitro anti-SARS-CoV-2 activity (low micromolar EC50). These compounds exhibited low toxicity, indicating potential for further development. Additionally, we employed computational tools like molecular docking and QSAR models to analyze protein-ligand interactions. These findings represent a significant step forward in the search for effective antiviral treatments and have great potential to impact the development of new broad-spectrum antiviral drugs.

biochemistry↗

bioRxiv2023

Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types

The human genome contains millions of candidate cis-regulatory elements (CREs) with cell-type-specific activities that shape both health and myriad disease states. However, we lack a functional understanding of the sequence features that control the activity and cell-type-specific features of these CREs. Here, we used lentivirus-based massively parallel reporter assays (lentiMPRAs) to test the regulatory activity of over 680,000 sequences, representing a nearly comprehensive set of all annotated CREs among three cell types (HepG2, K562, and WTC11), finding 41.7% to be functional. By testing sequences in both orientations, we find promoters to have significant strand orientation effects. We also observe that their 200 nucleotide cores function as non-cell-type-specific on switches providing similar expression levels to their associated gene. In contrast, enhancers have weaker orientation effects, but increased tissue-specific characteristics. Utilizing our lentiMPRA data, we develop sequence-based models to predict CRE function with high accuracy and delineate regulatory motifs. Testing an additional lentiMPRA library encompassing 60,000 CREs in all three cell types, we further identified factors that determine cell-type specificity. Collectively, our work provides an exhaustive catalog of functional CREs in three widely used cell lines, and showcases how large-scale functional measurements can be used to dissect regulatory grammar.

genomics↗

bioRxiv2023

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of Oxford Nanopore Technologies (ONT) PromethION sequencing, including those using proximity ligation and show that newer, higher accuracy ONT reads substantially improve assembly quality.

bioinformatics↗