Biology subjects

Pan, Y.

Publications and source records attributed to Pan, Y..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism

Circadian clock genes are emerging targets in many types of cancer, but their mechanistic contributions to tumor progression are still largely unknown. This makes it challenging to stratify patient populations and develop corresponding treatments. In this work, we show that in breast cancer, the disrupted expression of circadian genes has the potential to serve as biomarkers. We also show that the master circadian transcription factors (TFs) BMAL1 and CLOCK are required for the proliferation of metastatic mesenchymal stem-like (mMSL) triple-negative breast cancer (TNBC) cells. Using currently available small molecule modulators, we found that a stabilizer of cryptochrome 2 (CRY2), the direct repressor of BMAL1 and CLOCK transcriptional activity, synergizes with inhibitors of proteasome, which is required for BMAL1 and CLOCK function, to repress a transcriptional program comprising circadian cycling genes in mMSL TNBC cells. Omics analyses on drug-treated cells implied that this repression of transcription is mediated by the transcription factor binding sites (TFBSs) features in the cis-regulatory elements (CRE) of clock-controlled genes. Through a massive parallel reporter assay, we defined a set of CRE features that are potentially repressed by the specific drug combination. The identification of cis-element enrichment might serve as a new concept of defining and targeting tumor types through the modulation of cis-regulatory programs, and ultimately provide a new paradigm of therapy design for cancer types with unclear drivers like TNBC.

cancer biology↗

bioRxiv2024

Enhancement of spatial learning by 40 Hz visual stimulation requires parvalbumin interneuron-dependent hippocampal neurogenesis

Acute and short-term rhythmic 40 Hz light flicker stimulation has shown promising results in alleviating cognitive impairments in mouse models of Alzheimers disease (AD), stroke, and autism spectrum disorders (ASD). Understanding the long-term impacts and underlying mechanisms is crucial to progress this approach for potential human therapeutic applications. Here, we show that prolonged exposure to 40 Hz light flicker (1 hour per day for 30 days) significantly improved spatial learning and neurogenesis in the dentate gyrus (DG) without harmful behavioral side effects. Mice with transgenic deletion of doublecortin-positive cells (DCXDTR) in the adult hippocampus failed to exhibit enhanced neurogenesis and spatial learning with 40 Hz stimulation. Inactivation or knockout of GABAergic parvalbumin (PV) interneurons reduced the effects of 40 Hz entrainment and neurogenesis enhancement. Mechanistically, the stimulation did not alter the regional microvessel blood flow but significantly raised PV excitability and GABA levels and enhanced inhibitory transmission in the DG. Blocking GABAA receptors reversed the improvements in spatial learning and neurogenesis. These data showed that long-term exposure to 40 Hz light flicker enhances spatial learning through PV-dependent adult neurogenesis, which requires elevated GABA as a critical neurochemical mechanism for sustaining adult neurogenesis. In briefRhythmic 40 Hz light flicker alleviates cognitive impairments in diverse animal models of neurological diseases. Understanding its long-term effects and mechanisms is vital for advancing its therapeutic potential for humans. Here, we show that prolonged exposure to this flicker improves spatial learning and boosts adult neurogenesis in the dentate gyrus. Activation of PV interneurons and GABAergic support for the newborn immature neurons underlie this effect, demonstrating lasting benefits for the treatment of neurological diseases. HighlightsO_LILong-term exposure to 40 Hz light flicker significantly improved spatial learning and neurogenesis in the hippocampus, devoid of adverse effects. C_LIO_LIThe 40 Hz light flicker evoked adult neurogenesis requires the activity of GABAergic inhibitory PV interneurons. C_LIO_LIThe 40 Hz light flicker raised GABA levels and enhanced inhibitory transmission in the DG. C_LIO_LIIncreased GABA serves as a vital neurochemical mechanism to support adult neurogenesis. C_LI

neuroscience↗

bioRxiv2024

The under-recognized dominance of magnetosome gene cluster-containing bacteria in oxygen-stratified freshwater ecosystems

Magnetotactic bacteria (MTB) capable of magnetosome organelle biomineralization and magnetotaxis are widespread in chemically stratified aquatic environments. Conventionally, it has long been considered that the overall abundance of MTB in microbiota is not very high and that Magnetococcia is the most frequently identified and predominant MTB members. However, the diversity and distribution of MTB in chemically stratified environments remain elusive due to the lack of large-scale systematic analyses. Here we conduct a comprehensive survey of genomes containing magnetosome gene clusters (MGCs), a group of genes responsible for magnetosome biomineralization and magnetotaxis, in 267 metagenomes from 38 oxygen-stratified freshwater environments. A total of 63 MGC-containing genomes belonging to eight bacterial phyla are reconstructed, including the newly identified Myxococcota. We discover an unexpectedly high relative abundance of putative MTB (up to 15.4% of metagenomic reads) in hypoxic and anoxic water columns, in which Deltaproteobacteria, rather than traditionally considered Magnetococcia, are the most ubiquitous and predominant MGC-containing bacteria. Our analysis reveals a depth-specific taxonomy and function of MGC-containing bacteria in stratified water columns shaped by physicochemical conditions. These findings underscore the unrecognized ecophysiological importance of MTB in freshwater ecosystems.

microbiology↗

bioRxiv2024

Turn `noise' to signal: accurately rectify millions of erroneous short reads through graph learning on edit distances

Although the per-base erring rate of NGS is very low at 0.1% to 0.5%, the percentage/probability of erroneous reads in a short-read sequencing dataset can be as high as 10% to 15% or in the number of millions. Correction of these wrongly sequenced reads to retrieve their huge missing value will improve many downstream applications. As current methods correct only some of the errors at the cost of introducing many new errors, we solve this problem by turning erroneous reads into their original states, without bringing up any non-existing reads to keep the data integrity. The novelty of our method is originated in a computable rule translated from PCR erring mechanism that: a rare read is erroneous if it has a neighbouring read of high abundance. With this principle, we construct a graph to link every pair of reads of tiny edit distances to detect a solid part of erroneous reads; then we consider them as training data to learn the erring mechanisms to identify possibly remaining hard-case errors between pairs of high-abundance reads. Compared with state-of-the-art methods on tens of datasets of UMI-based ground truth, our method has made a remarkably better performance under 19 metrics including two entropy metrics that measure noise levels in a dataset. Case studies found that our method can make substantial impact on genome abundance quantification, isoform identification, SNP profiling, and genome editing efficiency estimation. For example, the abundance level of the reference genome of SARS-CoV-2 can be increased by 12% and that of Monkeypox can be boosted by 52.12% after error correction. Moreover, the number of distinct isomiRs is decreased by 31.56%, unveiling there are so many previously identified isomiRs that are actually sequencing errors. Author summaryDetecting short-read sequencing errors and correcting the related erroneous reads is a long-standing problem in bioinformatics. Current error correction algorithms correct only small parts of the errors but simultaneously introduce thousands of non-existing sequences. We present a new method to rectify erroneous reads under 300 bp produced by PCR-involved miRNA-sequencing, small RNA sequencing, or paired-end RNA sequencing, regardless of platform or sample type. Our method is the first kind considering the PCR erring mechanism and machine learning technique to improve sequencing data quality by turning millions of erroneous short reads into their original state without bringing up any non-existing sequences into the read set. Our error correction method can make a significant impact on a wide range of cutting-edge downstream applications. The observations and advantages in the case studies lay down strong evidence to question the accuracies of current downstream research outcomes and open new avenues to conduct downstream analysis whenever short-read data are adopted.

bioinformatics↗

bioRxiv2024

AncestryPainter 2.0: Visualizing ancestry composition and admixture history graph

To effectively depict the results of population genetics studies, it is essential to present ancestry composition and genetic distance. The growing amount of genomic data prompted us to design AncestryPainter 1.0, a Perl program to display the ancestry composition of numerous individuals using a rounded graph. Motivated by the requests of users in practical applications, we updated AncestryPainter to version 2.0 by coding in an R package and improving the layout, providing more options and compatible statistical functions for graphing. In particular, AncestryPainter 2.0 implements a method admixture history graph (AHG) to infer the admixture sequence of multiple ancestry populations, and allows for multiple pie charts at the center of the graph to display the ancestry composition of more than one target population. We also introduced an additional graphing module to visualize genetic distance through radial bars of varying lengths surrounding a core. Visualization functions per se have been enhanced in this update as well. Furthermore, AncestryPainter 2.0 includes two statistical modules to 1) merge ancestry proportion matrices and 2) infer admixture sequences through correlation analyses. AncestryPainter 2.0 is publicly available at https://github.com/Shuhua-Group/AncestryPainterV2 and https://pog.fudan.edu.cn/#/Software.

genetics↗

bioRxiv2024

collectNET: a web server for integrated inference of cell-cell communication network

SummaryCell-cell communication through ligand-receptor pairs forms the cornerstone for complex functionalities in multicellular organisms. Deciphering such intercellular signaling can contribute to un-raveling disease mechanisms and enables targeted therapy. Nonetheless, notable biases and inconsistencies are evident among the inferential outcomes generated by current methods for inferring cell-cell communication network. To fill this gap, we developed collectNET (http://health.tsing-hua.edu.cn/collectnet) as the first web server for efficiently inferring the cell-cell communication network, with efficient calculation, hierarchical browsing, comprehensive statistics, advanced searching, and intuitive visualization. collectNET provides a reliable online inference service with prior knowledge of three public ligand-receptor databases and systematic integration of three mainstream inference methods. Additionally, collectNET has assembled a human cell-cell communication atlas, including 126,785 significant communication pairs based on 343,023 single cells. We anticipate that collectNET will benefit researchers in gaining a more holistic understanding of cell development and differentiation mechanisms. Availability and ImplementationcollectNET is freely available at http://health.tsinghua.edu.cn/collectnet. Contactruijiang@tsinghua.edu.cn Supplementary informationSupplementary data are available at Bioinformatics online.

genomics↗

bioRxiv2024

LRRK2 G2019S mutation suppresses differentiation of Th9 and Treg cells via JAK/STAT3

The Leucine-rich repeat kinase-2 (LRRK2) G2019S mutation, resulting in aberrantly enhanced kinase activity, is one of the well-recognized genetic risk factors in Parkinsons Disease (PD). Increased LRRK2 activity was also observed in immune cells from PD patients. Emerging results have also unveiled an upsurge in -synuclein (-syn)-specific CD4+ T cell responses in PD patients. Given that LRRK2 mutations in PD are germline mutations, there are unmet meets to explore whether LRRK2 G2019S mutation contributes to the pathogenesis of PD via altering CD4+ T-cell functions. To fill this knowledge gap, we generated a new T cell receptor (TCR) transgenic mouse strain bearing LRRK2 G2019S knock-in mutation, OT-II/LRRK2 (Refer to Mut). As CD4+ T cells from OT-II mice specifically recognize ovalbumin, this new strain enables us to explore the impact of LRRK2 G2019S mutation on T-cell functions in an antigen-specific manner. We found that the abundance and proliferation of major immune subsets in spleen tissue from Mut mice are comparable to wild-type (OT-II, Refer to WT) control. However, when we characterized T cell differentiation in these two strains, T cells derived from Mut mice displayed increased Th2 differentiation (IL-4) and decreased Th9 (IL-9) and Treg (Foxp3+ %) differentiation. LRRK2 G2019S mutation significantly altered the expression levels of master transcription factors (TFs) for T cell differentiation. Specifically, Mut T cells displayed an increase in mRNA expression of Gata3 (TF for Th2), a decrease in expression of Irf4 and Foxp3 (TFs for Th9 and Treg, respectively). Mechanistically, LRRK2 mutation decreased IL-9 production and Treg cell population through the JAK/STAT3 signaling. In conclusion, LRRK2 plays a critical role in regulating T cell differentiation, warranting further studies to evaluate the impacts of altered T cell differentiation led by LRRK2 mutation in dopaminergic neuron damages.

immunology↗

bioRxiv2024

A computational and multi-brain signature for aberrant social coordination in schizophrenia

Social functioning impairment is a core symptom of schizophrenia (SCZ). Yet, the computational and neural mechanisms of social coordination in SCZ under real-time and naturalistic settings are poorly understood. Here, we instructed patients with SCZ to coordinate with a healthy control (HC) in a joint finger-tapping task, during which their brain activity was measured by functional near-infrared spectroscopy simultaneously. The results showed that patients with SCZ exhibited poor rhythm control ability and unstable tapping behaviour, which weakened their interpersonal synchronization when coordinating with HCs. Moreover, the dynamical systems modelling revealed disrupted between-participant coupling when SCZ patients coordinated with HCs. Importantly, increased inter-brain synchronization was identified within SCZ-HC dyads, which positively correlated with behavioural synchronization and successfully predicted dimensions of psychopathology. Our study suggests that SCZ individuals may require stronger neural alignment to compensate for deficiency in their coordination ability. This hyperalignment may be relevant for developing inter-personalized treatment strategies.

neuroscience↗

bioRxiv2024

A site-wise reliability analysis of the ABCD diffusion fractional anisotropy data, impact of the scanner and analytical pipeline

The Adolescent Brain and Cognitive Development (ABCD) project is the largest study of adolescent brain development. ABCD longitudinally tracks 11,868 participants aged 9-10 years from 21 sites using standardized protocols for multi-site MRI data collection and analysis. While the multi-site and multi-scanner study design enhances the robustness and generalizability of analysis results, it may also introduce non-biological variances including scanner-related variations, subject motion, and deviations from protocols. ABCD imaging data were collected biennially within a period of ongoing maturation in cortical thickness and integrity of cerebral white matter. These changes can bias the classical test-retest methodologies, such as intraclass correlation coefficients (ICC). We developed a site-wise adaptive ICC (AICC) to evaluate the reliability of imaging-derived phenotypes while accounting for ongoing brain development. AICC iteratively estimates the population-level age-related brain development trajectory using a weighted mixed model and updates age-corrected site-wise reliability until convergence. We evaluated the test-retest reliability of regional fractional anisotropy (FA) measures from diffusion tensor imaging and cortical thickness (CT) from structural MRI data for each site. The mean AICC for 20 FA tracts across sites was 0.61{+/-}0.19, lower than the mean AICC for CT in 34 regions across sites, 0.76{+/-}0.12. Remarkably, sites using Siemens scanners consistently showed significantly higher AICC values compared to those using GE/Philips scanners for both FA (AICC=0.71{+/-}0.12 vs 0.46{+/-}0.17, p<0.001) and CT (AICC=0.80{+/-}0.10 vs 0.69{+/-}0.11, p<0.001). These findings demonstrate site-and-scanner related variations in data quality and underscore the necessity for meticulous data curation in subsequent association analyses.

neuroscience↗

bioRxiv2024

An Engineered IGF2 Mutant for Lysosomal Targeting Chimeras Development and Membrane Proteins Degradation

Lysosome-targeting chimeras (LYTACs) have emerged as a promising strategy for targeted degradation of membrane proteins, offering potential applications in drug development. Currently, two main methods for developing LYTACs exist: chemically modified antibodies [1-2] and wild-type insulin-like growth factor 2 (IGF2) fusion proteins (iLYTACs) [3]. However, the fusion of the IGF2 arm within iLYTACs carries the risk of activating IGF1R tyrosine kinase activity and promoting tumor development. To address this concern, we introduce eiLYTACs, a technology that employs engineered IGF2 fusion antibodies to induce degradation of endogenous membrane proteins. Compared to the wild-type IGF2, the engineered IGF2 mutant exhibited minimal binding affinity for IGF1R but demonstrated a significant 100-fold increase in its binding affinity for IGF2R. In contrast to wild-type IGF2, which promotes tumor growth, the cells incubated with the engineered IGF2 showed no stimulation of tumor growth. The eiLYTACs strategy effectively inhibits tumor cell proliferation by degrading specific targets, resulting in a significant reduction in xenograft tumor size in experimental nude mice. More interestingly, our research revealed that eiLYTACs simultaneously degrade both homo- and heterodimers of disease-relevant proteins,which offer a promising strategy to address the activation of compensatory bypass signaling pathways, drug resistance, and tumor heterogeneity.

biochemistry↗

bioRxiv2024

Threshold-Free Network-Oriented Statistics in Neuroscience

Network neuroscience has emerged as an indispensable tool for studying brain structure and function. Currently, the network-based statistic (NBS) procedure is widely used for dealing with massive multiple testing/comparison problems in brain networks. However, the NBS requires choosing a hard cluster-forming threshold, lacking objective rules. A powerful and flexible statistical framework is urgently needed with growing interest in finer-grained network explorations across modalities and scales. Here, we introduce a permutation-based framework--"Threshold-Free Network-Oriented Statistics" (TFNOS). It integrates two "threshold-free" pathways: traversing all cluster-forming thresholds (TT) and using predefined clusters (PC). The TT procedure, building upon the threshold-free network-based statistics, requires setting additional parameters. The PC procedures comprise six variants given the degree of freedom in pooling data, null distribution construction, and controlled error rate. Using numerical simulations, we evaluated the performance of the TT procedure under 600 parameter combinations, then benchmarked TFNOS procedures and baselines across different topologies of effects, sample sizes, and effect sizes, and finally provided illustrative examples with real data. We offer recommended parameter values that allow the TT procedure to stably maintain leading power, while empirically controlling the false discovery rate (FDR) beyond only weakly controlling the familywise error rate (FWER). Notably, the relevant parameters commonly employed in the field appear overly liberal. Furthermore, for the PC procedures, FDR-controlling variants showed improved power compared to FWER-controlling variants, and some of them are simple but do not compromise power. The nonparametric PC procedures allow the selection of any test statistics considered appropriate. Overall, the TFNOS is a generalized framework for inference on edges/nodes of undirected/directed brain networks. We provide empirical and principled criteria for selecting appropriate procedures and may enhance the reproducibility and sensitivity of future brain research.

neuroscience↗

bioRxiv2023

Electrostatic-driven Interactions Enhance Intratumoral Retention and Antitumor Efficacy of Immune Checkpoint Blockade Antibodies

Tumor extracellular matrix (ECM) forms a net negative charged network that interacts with and hinders the transport of molecules partly based on electrostatic interactions. The focus on drug delivery in solid tumors has traditionally been on developing neutral charge coatings to minimize interactions with the ECM for improved transport. In contrast to this prior work, we recently found a cationic peptide that interacted electrostatically with the negatively charged components of the ECM, resulting in enhanced uptake and retention of nanoparticles in tumor ECM and tumor tissue. Based on this previous study, here, we hypothesize that the electrostatically driven interactions of the cationic peptide will improve the binding and retention of immune checkpoint blockade antibodies (ICBs), ultimately enhancing their antitumor immunogenic responses. We prepared peptide antibody (Ab) conjugates by conjugating the cationic peptide to ICBs, anti-cytotoxic T lymphocyte antigen 4 ({propto}-CTLA4) and anti-programmed cell death ligand-1 ({propto}-PD-L1) Abs, using copper-free click chemistry. We confirmed an average of 1 - 2 peptides per Ab. The cationic peptide electrostatically interacted with the net negatively charged tumor ECM and improved the binding of the Abs to the tumor ECM without affecting their antigen recognition capacities. Modifying the Abs due to cationic peptide conjugation reduced the systemic exposure of the Abs and did not induce treatment-related toxicities. We quantified a significantly higher population of tumor-infiltrating CD8+ T cells and a significant depletion of regulatory T cells in the tumor and tumor-draining lymph nodes upon peptide conjugation, which resulted in a better therapeutic outcome of the ICBs. ONE SENTENCE SUMMARYElectrostatic interaction-based intratumoral retention enhances antitumor responses of immune checkpoint blockade antibodies upon local administration.

bioengineering↗

bioRxiv2023

Chlamydial protease-like activating factor targets SLC7A11 for degradation to induce ferroptosis and facilitate dissemination.

Chlamydia trachomatis, the most prevalent bacterial agent of sexually transmitted infections, possesses remarkable capacities for dissemination within the host, leading to reproductive health complications. The release of progeny through the orchestrated lysis of host cells plays a crucial role in Chlamydia dissemination, but the underlying molecular mechanisms remain largely elusive. Here, we uncovered a novel mechanism by which Chlamydia induces host cells ferroptosis to facilitate its dissemination. This process involves the degradation of host protein SLC7A11 by the chlamydial protease-like activating factor (CPAF), resulting in glutathione depletion, oxidative damage, and subsequent host cell lysis characterized by lipid peroxidation. Infection with CPAF-deficient strain fails to induce host cells ferroptosis, leading to restricted progeny release. Importantly, inhibiting ferroptosis effectively limits the release of Chlamydia progeny, highlighting its potential as a therapeutic strategy for controlling Chlamydia dissemination. These findings provide insights into the chlamydial conserved dissemination strategy and enhance understanding of its pathogenesis.

microbiology↗

bioRxiv2023

Site Effects in Multisite Fetal Brain MRI: Morphological Insights into Early Brain Development

BackgroundMultisite MRI studies have become prevalent given their advantage in revealing reliable biological or clinical findings. Adult and adolescent multisite studies have demonstrated inevitable site-related non-biological effects that introduce bias. However, the site effect on fetal brain MRI remains unknown. PurposeTo identify crucial acquisition factors affecting fetal brain structural measurements and developmental patterns, while assessing the effectiveness of existing harmonization methods in mitigating site effects. Materials and MethodsBetween May 2017 and March 2022, T2-weighted fast spin-echo sequences in-utero MRI were performed in healthy fetuses from prospectively recruited pregnant volunteers on four different scanners at four sites. A generalized additive model (GAM) was used to quantitatively assess site effects, including field strength (FS), manufacture (M), in-plane resolution (R), and slice thickness (ST), on subcortical volume and cortical morphological measurements, including cortical thickness, curvature, and sulcal depth. Growth models were selected to elucidate developmental trajectories of these morphological measurements. Welchs test was performed to evaluate the influence of site effects on developmental trajectories. ComBat-GAM harmonization method was applied to mitigate site-related biases. ResultsThe final analytic sample consisted of 340 MRI scans from 218 fetuses (mean gestational age, 30.1 weeks {+/-} 4.4 [range, 21.7-40 weeks]). GAM results showed that low FS and low spatial resolution led to overestimations in selected brain regions of subcortical volumes and cortical morphological measurements, and cortical measurements were more susceptible to site effects than subcortical volumes. Only the peak cortical thickness in developmental trajectories was significantly influenced by the effects of FS and R. Notably, ComBat-GAM harmonization effectively removed site effects while preserving developmental patterns. ConclusionOur findings pinpointed the key acquisition factors in in-utero fetal brain MRI and underscored the necessity of data harmonization when pooling multisite data for fetal brain morphology investigations.

bioengineering↗

bioRxiv2023

Towards fNIRS Hyperfeedback: A Feasibility Study on Real-Time Interbrain Synchrony

Social interaction is of fundamental importance to humans. Prior research has highlighted the link between interbrain synchrony and positive outcomes in human social interaction. Neurofeedback is an established method to train ones brain activity and might offer a possibility to increase interbrain synchrony. Consequently, it would be advantageous to determine the feasibility of creating a neurofeedback system for enhancing interbrain synchrony to benefit human interaction. In this study, we investigated whether the most widely employed metric for interbrain synchrony, namely wavelet transform coherence, can be assessed accurately in near real-time using functional near-infrared spectroscopy (fNIRS), which is recognized for its mobility and ecological suitability for interactive research. To this end, we have undertaken a comprehensive approach encompassing simulations and a re-evaluation of two human-interaction datasets. Our findings indicate the potential for a stable near real-time measurement of wavelet transform coherence for integration durations of about one minute. This would align well with the methodology of an intermittent neurofeedback procedure. Our investigation lays the technical foundation for an fNIRS-based system to measure interbrain synchrony in near real-time. This advancement is crucial for the future development of a neurofeedback training system tailored to enhance interbrain synchrony to potentially benefit human interaction.

neuroscience↗

bioRxiv2023

Molecular and neuronal mechanisms governing sexually dimorphic prioritization of innate behaviors

Males and females display dimorphic innate behaviors and further prioritize them differently. How the sexually dimorphic behavioral prioritization is mediated is poorly understood. In Drosophila, around 60 pairs of pC1 neurons in males and 6 pairs in females control sexually dimorphic behaviors. We show that an increase of pC1 activity determines the sequential execution of behaviors such as sex, aggression, sleep, and feeding in a sex-specific way. We identify distinct subsets of pC1 neurons in both males and females that regulate different behaviors. We further discover diuretic hormone 44 (DH44) and acetylcholine (ACh) as co-transmitters in pC1 neurons. ACh promotes the execution of each behavior in both sexes, whereas DH44 functions in a sex-specific and activity-dependent manner to establish the sexually dimorphic behavioral outputs. These findings provide a framework for understanding the molecular and cellular mechanisms underlying sexually dimorphic prioritization of innate behaviors.

neuroscience↗

bioRxiv2023

A DNA condensation code for linker histones

Linker histones play an essential role in chromatin packaging by facilitating compaction of the 11-nm fibre of nucleosomal "beads on a string". The result is a heterogeneous condensed state with local properties that range from dynamic, irregular and liquid-like, to stable and regular structures (the 30-nm fibre), which in turn impact chromatin-dependent activities at a fundamental level. The properties of the condensed state depend on the type of linker histone, particularly on the highly disordered C-terminal tail, which is the most variable region of the protein, both between species, and within the various subtypes and cell-type specific variants of a given organism. We have developed an in-vitro model system comprising linker histone tail and linker DNA, which although very minimal, displays surprisingly complex behaviour, and is sufficient to model the known states of linker-histone-condensed chromatin: disordered "fuzzy" complexes ("open" chromatin), dense liquid-like assemblies (dynamic condensates) and higher-order structures (organised 30-nm fibres). A crucial advantage of such a simple model is that it allows the study of the various condensed states by NMR, CD and scattering methods. Moreover, it allows capture of the thermodynamics underpinning the transitions between states through calorimetry. We have leveraged this to rationalise the distinct condensing properties of linker histone subtypes and variants across species that are encoded by the amino acid content of their C-terminal tails. Three properties emerge as key to defining the condensed state: charge density, lysine/arginine ratio, and proline-free regions, and we evaluate each separately using a strategic mutagenesis approach.

biophysics↗

bioRxiv2023

Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity

Dysregulation of liver metabolism associated with obesity during feeding and fasting leads to the breakdown of metabolic homeostasis. However, the underlying mechanism remains unknown. Here, we measured multi-omics data in the liver of wild-type and leptin-deficient obese (ob/ob) mice at ad libitum feeding, and constructed a differential regulatory trans-omic network of metabolic reactions. We compared the trans-omic network at feeding with that at 16 h-fasting constructed in our previous study. Intermediate metabolites in glycolytic and nucleotide metabolism decreased in ob/ob mice at feeding but increased at fasting. Allosteric regulation reversely shifted between feeding and fasting, generally showing activation at feeding while inhibition at fasting in ob/ob mice. Transcriptional regulation was similar between feeding and fasting, generally showing inhibiting transcription factor regulations, activating enzyme protein regulations in ob/ob mice. The opposite metabolic dysregulation between feeding and fasting characterizes breakdown of metabolic homeostasis associated with obesity.

systems biology↗