Biology subjects

zhang, X.

Publications and source records attributed to zhang, X..

9 recordsLinked to original sources

bioRxiv2026

Transcription factors read a second regulatory code in chromatin

Transcription factors (TFs) decode gene regulatory information written in DNA, yet how this vocabulary is interpreted within chromatin remains largely unexplored. Here, using an upgraded NCAP-SELEX platform, we systematically map the nucleosomal DNA recognition landscapes of 269 human TFs. We uncover a widespread, chromatin-dependent mode of sequence recognition: many TFs recognize motifs on nucleosomal DNA that are distinct from their canonical naked-DNA binding sites, revealing that nucleosome architecture encodes a second gene regulatory code in chromatin. Cryo-electron microscopy structures of TF-nucleosome complexes demonstrate that this second code is read through a combination of nucleosome-induced DNA deformation and direct protein-histone contacts. Functional analyses show that these chromatin-encoded motifs actively promote chromatin accessibility and drive cell-type-specific cis-regulatory activity in vivo. Strikingly, a single TF can deploy its canonical and nucleosome-derived motif repertoires to partition and govern entirely distinct physiological programs. Together, our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture. This chromatin-encoded layer of regulatory information fundamentally expands our understanding of how TF specificity is achieved and how gene regulatory networks are wired in multicellular organisms.

systems biology↗

bioRxiv2026

ChemoCalib: multiblock PLS calibration of genome-scale metabolic models improves flux prediction over expression-only integration

MotivationConstraint-based metabolic modeling faces a calibration gap: genome-scale metabolic models (GEMs) integrated with transcriptomics alone rely on expression-to-flux heuristics (E-Flux, GIMME, iMAT, MOMENT) that ignore cross-omics co-variance structure and lack statistical mechanisms for propagating omics uncertainty into reaction bounds, yielding flux predictions with limited agreement to 13C metabolic flux analysis (MFA) measurements. ResultsWe present Chemo-Calib, a multiblock PLS (MB-PLS) framework that calibrates GEM reaction bounds from the shared latent structure of metabolomics, transcriptomics, and proteomics data. On 11 E. coli 13C-MFA reference conditions spanning the Keio fluxome and Holm 2010 datasets, ChemoCalib constrained FBA on iJO1366 achieves a Spearman{rho} = 0.461 overall (up to 0.523 in PPP) and Pearson r of 0.49-0.58 across central carbon pathways, with statistically significant improvement over expression-only baselines including E-Flux2 and SPOT (p < 0.05, Holm-corrected). The latent-to-constraint mapping employs GPR-aware VIP aggregation (Algorithm 1) to project multi-omics latent scores onto genome-scale reaction bounds without heuristic thresholding. An optional in-silico active learning loop (relegated to Supplementary Material) further tightens calibration through virtual experiment selection. AvailabilityChemoCalib is open-source (MIT) at https://github.com/chemocalib/chemocalib with Docker support, a 5-minute tutorial, and pre-computed iJO1366 benchmarks. Preprint available at bioRxiv; code archived at Zenodo DOI: 10.5281/zenodo.21645890.

bioinformatics↗

bioRxiv2026

Spatiotemporally distinctive astrocytic and neuronal responses to repetitive intracortical microstimulation

Astrocytes are increasingly recognized as active modulators of neuronal synaptic transmission. Intracortical microstimulation (ICMS) is widely used to manipulate neuronal activity, yet the accompanying astrocytic responses remain poorly characterized. Using dual-color in vivo two-photon calcium imaging to simultaneously monitor neurons and astrocytes, we show that ICMS elicits astrocytic activation with spatiotemporal features that diverge from those of neurons. Astrocytes were recruited at stimulation intensities as low as 10A, thresholds sufficient to activate neurons, indicating that astrocytes robustly sense electrical perturbation. Unlike neurons, however, astrocytic responses were spatially heterogeneous and temporally variable across trials. At higher stimulation intensities (>=50A), astrocytic responsiveness, i.e., response peak amplitude, and number of responsive trials, progressively attenuated across repeated trials, in contrast to the stable and consistent neuronal responses. Although neuronally driven, astrocytes exhibited a distinct response profile under the same stimulation parameter, revealing a unique component of electrically evoked cortical activity that underscores the importance of incorporating glial physiology into future neuroprosthetic strategies.

neuroscience↗

bioRxiv2025

Single-Cell and Population-Level Neuromodulation Dynamics in Dual-Electrode Intracortical Stimulation

In neuroprosthetics, intracortical microstimulation (ICMS) recruits cortical networks to evoke brain responses and sensory perceptions. However, multi-electrode ICMS often generates suboptimal percepts compared to single-electrode ICMS, suggesting nonlinear neuromodulation rather than simple summation by multi-electrode ICMS. Yet, the factors and mechanisms underlying this modulation remain poorly understood. To investigate multi-electrode ICMS, we combined two-photon calcium imaging with a well-controlled dual-electrode ICMS in the mouse visual cortex to investigate how neurons integrate converging ICMS inputs at varying intensities. We found that stimulation intensity significantly shapes neuromodulation at both single-cell and population levels. Specifically, low intensities (5-7 {micro}A) have a minimal effect on neural responses. At intermediate intensities (10-15 {micro}A), we observed diverse, nonlinear bipolar modulation--both enhancement and attenuation--at the single-cell level. However, we achieved net enhancement at the population level. At higher intensities (15-20 {micro}A), although the proportion of modulated neurons increased in both enhancement and attenuation directions, the net effect at the population level was neutral (zero modulation). Furthermore, neurons strongly responsive to single-electrode ICMS were more likely to be attenuated, while weaker responding cells exhibited enhanced modulation. The strongest neuromodulatory effects occur at intermediate spatial distances in between the two electrodes. Computational modeling based on spiking neural network composed of adaptive exponential integrate-and-field neurons implicated the importance of inhibitory network dynamics and network variability as key mechanisms. Our experimental data was used to train an advanced deep learning approach, which successfully predicted the neuromodulation patterns induced by dual-electrode ICMS. Our findings reveal intensity- and spatial-dependent rules of neuromodulation by ICMS, providing necessary insights to optimize multi-electrode ICMS for neuroprosthetic applications. Significance statementUnderstanding how cortical neurons integrate concurrent inputs from multi-electrode intracortical microstimulation (ICMS) is essential for advancing neuroprosthetic technologies. We show that dual-electrode ICMS evokes distinct, predictable neuromodulatory effects that depend on (i) stimulation intensity, (ii) a neurons baseline responsiveness to single electrode input, and (iii) its proximity to the electrodes. Low and intermediate intensity dual-electrode ICMS amplifies neural activity compared to single-electrode ICMS, whereas high-intensity stimulation leads to attenuation, limiting net activation.

neuroscience↗

bioRxiv2024

Spatially mismatched cerebral blood flow and neuronal activity by intracortical microstimulation

Intracortial microstimulation (ICMS) is widely used in brain-machine interface for neuroprosthetics, particularly with aims of restoring lost sensory and motor functions. However, it remains poorly understood whether neuronal and blood flow responses by ICMS are spatially and temporally matched, as well as their underlying mechanism. Neurovascular coupling (NVC) is the process by which neuronal activity regulates blood flow in the brain to meet local metabolic demands. A hypothetically suboptimal NVC by ICMS may exacerbate the neuronal survival near electrode, contributing to neurodegeneration. In this study, we used wide-field imaging, laser speckle imaging and two-photon imaging in transgenic mice expressing calcium fluorescent indicators in neurons or vascular mural cells to examine this hypothesis. Our results showed blood flow responses are delayed at peak time and prolonged in duration compared with neuronal responses. By varying the stimulation amplitudes, we found that low stimulation intensity lower than 50A preserved NVC. In contrast, high intensity stimulation caused spatially mismatched NVC, i.e. in the adjacent range within 200[~]400 m from electrode tip, elicited blood flow compromises but neuronal activities increase. Ca2+ is the key regulator of contractile tone of vascular mural cells. Our results showed that Ca2+ sensitivity at vascular mural cells, i.e. vessel diameter change per unit of Ca2+ change, was decreased in the adjacent region of electrode, which partially explained the compromised and mismatched NVC, and which likely further lead to ischemia and neurodegeneration. This study offers a new insight into ICMS-associated neuronal and vascular physiology, and provides an important implication towards optimal design of ICMS: low intensities is more neuroprotective than high intensities by preserving NVC and preventing ischemia. Our discoveries pave the way for new research consideration and contribute to the development of more advanced brain-machine interface.

neuroscience↗

bioRxiv2024

The neurovascular coupling response of the aged brain is brain-state dependent.

Brain aging lead to reduced cerebral blood flow and cognitive decline, but how normal aging affects neurovascular coupling (NVC) in the awake brain is unclear. Here, we investigated NVC in relation to calcium changes in vascular mural cells (VMCs) in awake adult and aged mice. We show that NVC responses are reduced and prolonged in the aged brain and that this is more pronounced at the capillary level than in arterioles. However, the overall NVC response, measured as the time integral of vasodilation, is the same in two age groups. In adult, but not in aged mice, the NVC response correlated with Ca2+ signaling in VMCs, while the overall Ca2+ kinetics were slower in aged than in adult mice. In particular, the rate of Ca2+ transport, and the Ca2+ sensitivity of VMCs were reduced in aged mice, explaining the reduced and prolonged vasodilation. Spontaneous locomotion was less frequent and reduced in aged mice as compared to young adult mice, and this was reflected in the slow but prolonged NVC and vascular Ca2+ responses. Taken together, our data characterize the NVC in the aged awake brain as slow but prolonged, and underscoring the importance of brain state in understanding age-related mechanisms.

neuroscience↗

bioRxiv2022

HSP90.6 is involved in grain filling via carbon and nitrogen metabolism in maize.

Carbon and nitrogen are the two most abundant nutrients in all living things, and their metabolism maintains normal plant growth. However, the molecular mechanism underlying carbon and nitrogen metabolism remains largely unknown. Here, we found that HSP90.6 is involved in the metabolism of carbon and nitrogen. We performed gene cloning and functional characterization of a maize EMS mutant ehsp90.6, whose kernels were small. HSP90.6 encodes heat shock protein 90.6, which has a single-amino acid mutation within its HATPase_c domain. Transcriptome profiling showed that the expression of amino acid biosynthesis- and carbon metabolism-related genes was significantly downregulated in hsp90.6. HSP90.6 is involved in the 26S proteasome degradation pathway, which affects nitrogen recycling to regulate amino acid synthesis; this occurs by interactions between HSP90.6 and the 26S proteasome subunits RPN6 and PBD2 (PRC2). The loss of HSP90.6 significantly reduced the activity of the 26S proteasome, resulting in the accumulation of ubiquitinated proteins and defects in nitrogen recycling. Moreover, HSP90.6 interacted with the 14-3-3 protein GF14-6 to participate in carbon metabolism. Together, these findings revealed that HSP90.6 regulates nutrient metabolism in maize seeds by affecting 26S proteasome-mediated nitrogen recycling and GF14-6-mediated carbon metabolism. One sentence summaryHSP90.6 is involved in nutrient metabolism via 26S proteasome-mediated protein degradation to promote nitrogen recycling and GF14-6 protein-mediated carbon metabolism. The author responsible for the distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/pages/General-Instructions) is Weibin Song (songwb@cau.edu.cn). HighlightsO_LIHATPase_c is necessary for HSP90.6 to regulate maize kernel development. C_LIO_LIHSP90.6 is involved in nitrogen recycling via the 26S proteasome degradation pathway. C_LIO_LIHSP90.6 interacts with the 14-3-3 protein GF14-6 to affect carbon metabolism. C_LI IN A NUTSHELLO_ST_ABSBackgroundC_ST_ABSSeeds are the main harvested organs of maize. Understanding the regulatory mechanism of grain filling is helpful to cultivate high-quality and high-yield maize. In the past few years, the regulatory network of grain filling has been explored through multiple means, including transcriptomic, proteomic and functional genomic techniques. Many genes that control grain filling through different mechanisms have been cloned, such as CTLP1 (Choline Transporter-like Protein 1), OS1 (Opaque Endosperm and Small Germ 1), and MN6 (Miniature Seed6). To identify new genes involved in maize grain filling, ethyl methanesulfonate (EMS) was used to induce mutations, and the ehsp90.6 mutant, which exhibited abnormal kernel development, was isolated by bulked segregant analysis RNA sequencing (BSR). QuestionWhy does the single-amino acid mutation of HSP90.6 affect grain size, and how does the loss of HSP90.6 affect grain filling? FindingsA single-amino acid mutant (ehsp90.6) and knockout mutant (hsp90.6) were obtained. We found that HSP90-6 was involved in the regulation of maize grain filling. A single-single amino acid mutation in the HATPase_c domain reduced the ATPase activity of HSP90.6, resulting in smaller grains. The functional loss of HSP90.6 resulted in the expression of amino acid biosynthesis- and carbon metabolism-related genes being significantly downregulated in hsp90.6. We indicated that HSP90.6 is involved in the 26S proteasome degradation pathway, which affects nitrogen recycling to regulate amino acid synthesis by interacting with the 26S proteasome subunits RPN6 and PBD2 (PRC2). Moreover, HSP90.6 was found to interact with the 14-3-3 protein GF14-6 to participate in carbon metabolism. Next stepsTo further verify that the interaction between HSP90.6 and 26S proteasome subunits and GF14-6 affects grain filling, knockout validation of RPN6, PBD2 (PRC2) and GF14-6 will be performed. In addition, since GF14-6 interacts with the phosphorylated proteins, we will determine the phosphorylation site of HSP90.6. Due to the important role of HSP90 family proteins in plant development, there are other regulatory pathways that need to be explored.

plant biology↗

bioRxiv2020

Structural and biochemical mechanisms of NLRP1 inhibition by DPP9

The nucleotide-binding domain (NBD) and leucine-rich repeat (LRR)-containing receptors (NLRs) mediate innate immunity by forming inflammasomes. Activation of the NLR protein NLRP1 requires auto-cleavage within its FIIND domain1-7. In resting cells, the dipeptidyl peptidase DPP9 interacts with NLRP1-FIIND and together with a related enzyme DPP8, suppresses spontaneous NLRP1 activation8,9. The mechanisms of DPP8/9-mediated NLRP1 inhibition, however, remain elusive. Here we provide structural and biochemical evidence demonstrating that rat NLRP1 (rNLRP1) interacts with rDPP9 in a stepwise manner to form a 2:1 complex. An auto-inhibited rNLRP1 molecule first interacts with rDPP9 via its ZU5 domain. This 1:1 rNLRP1-rDPP9 complex then captures the UPA domain of a second rNLRP1 molecule via a UPA-interacting site on DPP9 and dimeric UPA-UPA interactions with the first rNLRP1. The 2:1 rNLRP1-rDPP9 complex prevents NLRP1 UPA-mediated higher order oligomerization and maintains NLRP1 in the auto-inhibited state. Structure-guided biochemical and functional assays show that both NLRP1-binding and its enzymatic activity are required for DPP9 to suppress NLRP1, supporting guard-type activation of the NLR. Together, our data reveal the mechanism of DPP9-mediated inhibition of NLRP1 and shed light on activation of the NLRP1 inflammasome.

immunology↗

bioRxiv2020

Loss of Corneal Raver2 Expression in Aniridia Associated Keratopathy

PurposeThe aim of this study was to evaluate downstream factors of Pax6 associated with the aniridic corneal phenotype. We characterize the ocular expression of Raver2, a novel heterogeneous ribonucleoprotein (hnRNP). MethodsGenome wide microarrays of corneal RNA from non-aniridic mice (C57BL/6J and MRL/MpJ) and corneas from aniridia model, Pax6+/- (SEY) mice were performed. Raver2 expression profiles were validated using qPCR and western blot. Raver2 immunohistochemistry on corneas of Pax6+/- mice and aniridic humans were compared to control specimens, and insitu-hybridization was used to analyze developmental expression of Raver2. ResultsMicroarray analysis of corneal RNA identified Raver2 as the gene with the strongest differential expression profile across non-aniridic and aniridic mouse strains. Consistent with mouse data, we found that Raver2 is expressed at high levels in healthy human corneal epithelium, and is downregulated in the corneas of human aniridia patients. ConclusionsThese findings suggest that Raver2 has an evolutionarily conserved developmental role downstream of Pax6 in corneal development and maintenance.

developmental biology↗