Biology subjects

Deng, J.

Publications and source records attributed to Deng, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Multiplexing Light-Inducible Recombinases to Control Cell Fate, Boolean Logic, and Cell Patterning in Mammalian Cells

Light-inducible regulatory proteins are powerful tools to interrogate fundamental mechanisms driving cellular behavior. In particular, genetically encoded photosensory domains fused to split proteins can tightly modulate protein activity and gene expression. While light-inducible split protein systems have performed well individually, few multichromatic and orthogonal gene regulation systems exist in mammalian cells. The design space for multichromatic circuits is limited by the small number of orthogonally addressable optogenetic switches and the types of effectors that can be actuated by them. We developed a library of red light-inducible recombinases and directed patterned myogenesis in a mesenchymal fibroblast-like cell line. To address the limited number of light-inducible domains (LIDs) responding to unique excitation spectra, we multiplexed light-inducible recombinases with our Boolean Logic and Arithmetic through DNA Excision (BLADE) platform. Multiplexed optogenetic tools will be transformative for understanding the role of multiple interacting genes and their spatial context in endogenous signaling networks.

molecular biology↗

bioRxiv2024

Cardiac Reprogramming with Drug Resistance Alleviates Doxorubicin-induced Cardiotoxicity in Mice and Pigs

Doxorubicin (Dox)-induced cardiotoxicity represents a significant clinical adverse effect associated with cancer chemotherapy treatment. The systematic toxicity associated with the currently available drug dexrazoxane has limited its clinical utility. Inspired by cancer drug resistance mechanisms, we propose a novel strategy termed Transient overexpression of p-glycoprotein (P-gp) for Cardiac reprogramming (TopCare) to induce cardiac drug resistance as a treatment for cardiotoxicity. This approach involves reprogramming cardiomyocytes by delivering lipid nanoparticles (LNPs)-based mRNA therapeutics to induce temporary P-gp overexpression, which in turn reduces intracellular Dox levels and suppresses cytotoxic effects. Our results demonstrated that LNPs with P-gp mRNAs (P-gp LNPs) enhance P-gp expression in H9c2 cells, significantly lowering the cytotoxicity of both Dox and paclitaxel (PTX). In a mouse model with Dox-induced cardiotoxicity, it was observed that P-gp LNPs effectively promoted P-gp overexpression in cardiomyocytes, with a time-dependent decline in P-gp protein levels. This TopCare strategy resulted in improved survival rates, restored cardiac function, and reduced myocardial fibrosis and structural cardiac alterations. Furthermore, studies in large animals have shown that intrapericardial (iPC) injection of P-gp LNPs effectively mitigates adverse effects and restores cardiac function in pig models of Dox-induced cardiotoxicity. The significant cardioprotective effects achieved through cardiac drug resistance highlight the safety, efficacy, and clinical potential of the TopCare strategy for alleviating doxorubicin-induced cardiotoxicity.

bioengineering↗

bioRxiv2024

UniSPAC: A Unified Segmentation Framework for Proofreading and Annotation in Connectomics

Reconstructing dense neuronal connections from volume electron microscopy (vEM) images is a critical challenge in neuroscience, driving the development of various automatic neuron segmentation methods1. Although current state-of-the-art automated segmentation methods can achieve high segmentation accuracy, they still require substantial manual proofreading and rely heavily on labeled datasets, which are often scarce, particularly for non-model organisms. Here, we introduce a Unified Segmentation framework for Proofreading and Annotation in Connectomics (UniSPAC) by providing the interactive segmentation model in 2D-level and the neuron tracing model in 3D-level. UniSPAC-2D allows users to correct its segmentation errors through point-based prompts, combining segmentation and proofreading in a single framework. UniSPAC-3D automatically traces neurons segmented by UniSPAC-2D across image slices, significantly reducing human involvement. Furthermore, UniSPAC-2D and UniSPAC-3D models can facilitate the semi-automatic generation of labeled data for new species, eliminating the need for external annotation tools. The fresh annotated data generated during proofreading in turn optimizes the interactive model through an online learning strategy, reducing the labeling effort for novel species over time. UniSPAC outperforms the start-of-the-art Segment Anything Model (SAM) in Drosophila segmentation, achieving 47x higher efficiency, and surpasses ACRLSD in cross-species segmentation on zebra finch data.

neuroscience↗

bioRxiv2024

RetS senses neurotransmitter norepinephrine and adrenergic agents to regulate Pseudomonas aeruginosa virulence

Bacterial cells employ diverse mechanisms to perceive and respond to host-associated molecules, coordinate intracellular signal transduction, and engage in interkingdom communications. In this study, we firstly discovered that the adrenergic antagonist dronedarone (DDR) effectively suppresses quorum sensing (QS) and pathogenesis of the opportunistic pathogen P. aeruginosa. Further analysis revealed that DDR targets RetS, an bacterial surface receptor critical for suppressing the GacS/GacA two-component regulatory system (TCS). Interestingly, the adrenergic agonist norepinephrine (NE) was found to exert opposite effects against RetS, thereby reversing DDR-induced phenotypes in P. aeruginosa. Moreover, we identified the hinge region of RetSDISMED2 serves as a binding pocket of NE and DDR, which provides potential mechanisms of the antagonistic effect of NE and DDR. Our study demonstrated that NE promotes P. aeruginosa infections while DDR can serve as an anti-virulence compound against P. aeruginosa infections. Thus, RetS might serve as a bacterial adrenergic receptor which keeps the NE under constant surveillance. SignificanceSensing and recognition of host-derived molecules, as well as therapeutic drugs, are crucial for the survival of pathogens during infection process. The adrenergic drugs are well known to affect virulence and pathogenesis of the opportunistic pathogen Pseudomonas aeruginosa (P. aeruginosa). In this work, we have provided in-depth characterization of a Norepinephrine (NE) receptor in P. aeruginosa, the RetS membrane protein. NE is the-adrenergic agonist known as a stress hormone, exerts its activity through interaction with mammalian adrenergic receptors (AR). It has been shown that increased NE concentration during early sepsis can stimulate the growth of various Gram-negative and Gram-positive bacteria, including P. aeruginosa. We revealed that both adrenergic agonist NE and another adrenergic antagonist dronedarone (DDR) are able to interfering the RetS-GacS/GacA signaling cascade of P. aeruginosa and execute opposite impact on the pathogenesis of P. aeruginosa during infections.

microbiology↗

bioRxiv2024

Generation of a biosafety mouse model infection for SARS-CoV-2 replicon delivery particles

Animal models are essential for understanding the pathogenesis of SARS-CoV-2 and for developing therapeutic strategies. Replicon delivery particles (RDPs) were a component of trans-complementary systems for SARS-CoV-2, which is a safe and convenient tool in researching SARS-CoV-2 in animal biosafety level-II laboratory (ABSL-2). Here, we constructed a mouse model that conditional expressing SARS-CoV-2 N on the background of the K18-hACE2 KI mice. The SARS-CoV-2 N with flanked loxP-stop-loxP sequence was under the CAG promoter, and this cassette was knocked into the Tiger locus of mouse by CRISPR-Cas9 (K18-hACE2-N KI). By mating K18-hACE2-N KI mice with Cre tool mice, the offspring can express SARS-CoV-2 N (Cre-N-hACE2 KI) systemically and in a tissue-specific manner. Cre-N-hACE2 KI exhibited susceptibility to the SARS-CoV-2 {Delta}N-GFP/HBiT infection. The viral loads in lung exhibited a mountain-like trend, peaking at 4 days post-infection, and lung injuries can be observed. Overall, we demonstrated a mouse model infection for SARS-CoV-2 {Delta}N-GFP/HBiT to understand SARS-CoV-2 pathogenesis.

microbiology↗

bioRxiv2024

Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar

We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, weekly Malaise trap samples were collected at 203 locations within 100 sites in Sweden and at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of COI (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.

ecology↗

bioRxiv2024

Single-cell Landscape of Immune Cells in Blood and Skin in Psoriasis

BackgroundPsoriasis is a systemic inflammatory disease for which there is currently no cure, in part due to an incomplete understanding of its pathophysiology. MethodsTo better understand the immune response in psoriasis, we performed single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells (PBMCs) and on lesional and non-lesional skin samples from a cohort of 11 psoriasis patients and 8 healthy controls. Additionally, we conducted flow cytometry on PBMCs from a separate cohort of 13 psoriasis patients and 11 ankylosing spondylitis. FindingsOur study revealed altered immune signatures of specific myeloid and lymphocyte subsets in blood and skin, both in terms of cell numbers and gene expression. Specifically, we discovered elevated proportions of circulating CD14++ monocytes, increased expression of major histocompatibility complex (MHC) class II molecule by circulating CD16+ monocytes, as well as increased expression of genes related to skin homing and to pro-inflammatory responses in psoriasis by circulating plasmacytoid dendritic cells (pDCs). Circulating CD8+ T effector memory cells in psoriasis patients exhibited reduced abundance but increased skin-homing potential. In psoriatic lesions, we observed a hyperinflammatory myeloid-cell state and enrichment of IL17-producing cells with a tissue-resident memory T-cell signature. InterpretationThe changes in immune cell numbers and gene expression indicate a significant alteration in the immune landscape of psoriasis patients. This suggests that the immune system in psoriasis is reprogrammed, affecting both innate and adaptive branches. These findings provide new insights into the aberrant immune-cell signatures in the circulation and skin lesions in psoriasis, and thereby help to understand its pathophysiology. FundingThis study was financially supported by the National Natural Science Foundation of China (U23A6012), Science and Technology Planning Project of Guangzhou (2024A03J0055, 202206080005), Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine (ZYYCXTD-C-202204).

systems biology↗

bioRxiv2024

Shade Inhibits Cambial Activity in Populus Stems by the SPL16/SPL23-Mediated Cytokinin Pathway

Trees in natural forests or plantations often encounter neighbor proximity signal that negatively impacts wood production. However, the molecular basis underlying shade-regulation of vascular cambial activity during stem radial growth remains unknown in woody species. Here, we revealed that high stand density and simulated shade (low R/FR ratio) suppress the division and differentiation of cambial cells in poplar stems. A genome-wide screen for Populus SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes identified that SPL16 and SPL23 are preferentially expressed in the phloem and cambium, being downregulated by simulated shade. Knocking out SPL16/23 impaired cambial activity, whereas phloem-specific overexpression of SPL16 stimulated cambial proliferation and mitigated the shade-inhibition of cambial activity. Additionally, shade decreased bioactive cytokinin (CK) levels by suppressing the expression of CK biosynthesis genes IPT5a, IPT5b and LOG1b in poplar stems. Molecular and genetic studies reveled that SPL16/23 directly activate IPT5s/LOG1b expression to promote CK biosynthesis and cambial activity. Moreover, elevated miR156 expression in shade-treated stems regulated SPL16/23 at the post-transcriptional level, mediating shades effects on cambial activity. Collectively, our findings unravel that the miR156-SPL16/23-IPT5/LOG1-cytokinin pathway operates in the shade-mediated inhibition of cambial activity, providing potential targets for the genetic improvement of shade-tolerant trees.

plant biology↗

bioRxiv2024

Deep Generative Optimization of mRNA Codon Sequences for Enhanced Protein Production and Therapeutic Efficacy

Messenger RNA (mRNA) therapeutics show immense promise, but their efficacy is limited by suboptimal protein expression. Here, we present RiboDecode, a deep learning framework that generates mRNA codon sequences for enhanced mRNA translation. RiboDecode introduces several advances, including direct learning from large-scale ribosome profiling data and generative exploration of a large sequence space. In silico analysis demonstrates RiboDecode s robust predictive accuracy for unseen genes and cellular environments. In vitro experiments showed substantial improvements in protein expression, significantly outperforming past methods. In addition, RiboDecode enables mRNA design with consideration of cellular context and demonstrates robust performance across different mRNA formats, including m1{Psi}-modified and circular mRNAs, an important feature for mRNA therapeutics. In vivo mouse studies showed that optimized influenza hemagglutinin mRNAs induce ten times stronger neutralizing antibody responses against influenza virus compared to the unoptimized sequence. In an optic nerve crush model, optimized nerve growth factor mRNAs achieve equivalent neuroprotection of retinal ganglion cells at one-fifth the dose of the unoptimized sequence. Collectively, RiboDecode represents a paradigm shift from rule-based to a data-driven, context-aware approach for mRNA therapeutic applications, enabling the development of more potent and dose-efficient treatments.

bioinformatics↗

bioRxiv2024

Characterization of tumor heterogeneity through segmentation-free representation learning

The interaction between tumors and their microenvironment is complex and heterogeneous. Recent developments in high-dimensional multiplexed imaging have revealed the spatial organization of tumor tissues at the molecular level. However, the discovery and thorough characterization of the tumor microenvironment (TME) remains challenging due to the scale and complexity of the images. Here, we propose a self-supervised representation learning framework, CANVAS, that enables discovery of novel types of TMEs. CANVAS is a vision transformer that directly takes high-dimensional multiplexed images and is trained using self-supervised masked image modeling. In contrast to traditional spatial analysis approaches which rely on cell segmentations, CANVAS is segmentation-free, utilizes pixel-level information, and retains local morphology and biomarker distribution information. This approach allows the model to distinguish subtle morphological differences, leading to precise separation and characterization of distinct TME signatures. We applied CANVAS to a lung tumor dataset and identified and validated a monocytic signature that is associated with poor prognosis.

cancer biology↗

bioRxiv2024

Reusing excess staple oligonucleotides for economical production of DNA origami

DNA origami has enabled the development of responsive drug-delivery vehicles with precision features that were previously not attainable in bionanotechnology. To reduce the costs of creating therapeutics-scale amounts of DNA origami that need to bear costly modifications with high occupancy, we reused the excess staple oligonucleotides that are leftover from the folding process to fold additional origami. We determined that a DNA origami can be successfully folded with up to 80% cost savings by cyclic recovery and reuse of excess staple strands. We found evidence that higher quality staple strands are preferentially incorporated into origami, consistent with past reports, and therefore are preferentially depleted from the free-strand pool. The folding of DNA origami with staple strands that were reused up to eleven times was indistinguishable by our panel of assays versus a control folded with new strands, so long as the reused oligonucleotides were replenished each cycle with a small excess of fresh strands. We also observed a high degree of incorporation of guests on the DNA origami. By recovering, reusing, and replenishing excess staple oligonucleotides, it is possible to significantly lessen production costs to create well-formed origami, which is useful to allow more therapeutic designs to be tested.

synthetic biology↗

bioRxiv2024

Phylogenomics resolves the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha)

Planthoppers (Hemiptera: Fulgoromorpha) are a species-rich and globally distributed insect clade with high economic, ecological, and evolutionary importance. However, the relationships among planthopper lineages and families remain unclear. Previous efforts based on inconsistent morphological traits, a few genes, or limited sampling often resulted in conflicting tree topologies. Here, we used genome-level data to assemble 1164 nuclear single-copy genes and 13 mitochondrial protein-coding genes for 149 planthopper species representing 19 out of 21 extant families. Additional markers were added from published mitogenomes, expanding our sampling to 285 species. These markers were used for Maximum Likelihood-based tree inference and dating analyses. The newly inferred phylogenies validated well-accepted relationships and recovered novel placements. Taxonomic conclusions include the establishment of a new family Borysthenidae stat. rev. within Delphacoidea and a new superfamily Meenoploidea superfam. nov. including redefined Kinnaridae stat. rev. and Meenoplidae stat. rev., the confirmation of the monophyletic family Achilixiidae outside the Achilidae-Derbidae clade, and the transfer of tribes Lyncidini and Amyclini to Dictyopharidae and the genus Madagascaritia to Fulgoridae. The time analyses based on 57 nuclear markers and 30 fossils dated the origin of crown Fulgoromorpha back to Guadalupian, Permian ([~]263 Ma), close to the maximum constraint at 267.3 Ma, while applying an older root constraint resulted in an origin in Mississippian, Carboniferous ([~]332 Ma). While future sampling of unstudied fauna in unexplored regions or habitats may change the topology, the current phylogenomic analysis will serve as a solid foundation for research into planthopper ecology, evolution, and significance.

evolutionary biology↗

bioRxiv2024

The development of ecological systems along paths of least resistance

A long-standing question in biology is whether there are common principles that characterize the development of ecological systems (the appearance of a group of taxa), regardless of organismal diversity and environmental context. Classic ecological theory holds that these systems develop following a sequenced orderly process that generally proceeds from fast-growing to slow-growing taxa and depends on life-history trade-offs. However, it is also possible that this developmental order is simply the path with the least environmental resistance for survival of the component species and hence favored by probability alone. Here, we use theory and data to show that the order from fast-to slow-growing taxa is the most likely developmental path for diverse systems when local taxon interactions self-organize to minimize environmental resistance. First, we demonstrate theoretically that a sequenced development is more likely than a simultaneous one, at least until the number of iterations becomes so large as to be ecologically implausible. We then show that greater diversity of taxa and life histories improves the likelihood of a sequenced order from fast-to slow-growing taxa. Using data from bacterial and metazoan systems, we present empirical evidence that the developmental order of ecological systems moves along the paths of least environmental resistance. The capacity of simple principles to explain the trend in the developmental order of diverse ecological systems paves the way to an enhanced understanding of the collective features characterizing the diversity of life.

ecology↗

bioRxiv2024

Suppression of astrocyte BMP signaling improves fragile X syndrome molecular signatures and functional deficits

Fragile X syndrome (FXS) is a monogenic neurodevelopmental disorder with manifestations spanning molecular, neuroanatomical, and behavioral changes. Astrocytes contribute to FXS pathogenesis and show hundreds of dysregulated genes and proteins; targeting upstream pathways mediating astrocyte changes in FXS could therefore be a point of intervention. To address this, we focused on the bone morphogenetic protein (BMP) pathway, which is upregulated in FXS astrocytes. We generated a conditional KO (cKO) of Smad4 in astrocytes to suppress BMP signaling, and found this lessens audiogenic seizure severity in FXS mice. To ask how this occurs on a molecular level, we performed in vivo transcriptomic and proteomic profiling of cortical astrocytes, finding upregulation of metabolic pathways, and downregulation of secretory machinery and secreted proteins in FXS astrocytes, with these alterations no longer present when BMP signaling is suppressed. Functionally, astrocyte Smad4 cKO restores deficits in inhibitory synapses present in FXS auditory cortex. Thus, astrocytes contribute to FXS molecular and functional phenotypes, and targeting astrocytes can mitigate FXS symptoms.

neuroscience↗

bioRxiv2024

Enrichment of glycoRNAs using galactose oxidase, hydrazide chemistry, and glycosidase digestion

Ribonucleic acid (RNA), essential for protein production and immune function, undergoes glycosylation, a process that attaches carbohydrates to RNA, creating unique glycoRNAs. These sugar-coated RNA molecules regulate immune responses and may be related to immune disorders. However, studying them is challenging due to RNAs fragility. Therefore, a robust method for identifying glycosylated RNA is important. To address this, we optimized methods for enriching and identifying glycoRNAs, opening doors to explore their potential interactions with immune receptors and tumor suppression. Our approach involved investigating factors such as preservation solutions, enzyme buffers, digestion temperature, and incubation time. We successfully achieved efficient digestion of both N-linked and O-linked glycoRNAs at room temperature using 25 mM ammonium bicarbonate, demonstrating the effectiveness of this method. Additionally, RNA preservation in RNAlater at -80{degrees}C allows controlled release of glycoRNAs within hours. While sequential digestion of different glycoRNA types is possible, significant degradation occurs after the first enzyme step. Thus, we recommend separate harvesting for each type of glycoRNA. These optimized protocols, utilizing SPCgRNA and TnORNA methods, pave the way for further research on N- and O-glycoRNAs in health and disease.

biochemistry↗

bioRxiv2024

Improving Predictability, Test-Retest Reliability and Generalisability of Brain-Wide Associations for Cognitive Abilities via Multimodal Stacking

Brain-wide association studies (BWASs) have attempted to relate cognitive abilities with brain phenotypes, but have been challenged by issues such as predictability, test-retest reliability, and cross-cohort generalisability. To tackle these challenges, we proposed a machine-learning "stacking" approach that draws information from whole-brain magnetic resonance imaging (MRI) across different modalities, from task-fMRI contrasts and functional connectivity during tasks and rest to structural measures, into one prediction model. We benchmarked the benefits of stacking, using the Human Connectome Projects: Young Adults (n=873, 22-35 years old) and Human Connectome Projects-Aging (n=504, 35-100 years old) and the Dunedin Multidisciplinary Health and Development Study (Dunedin Study, n=754, 45 years old). For predictability, stacked models led to out-of-sample r[~].5-.6 when predicting cognitive abilities at the time of scanning, primarily driven by task-fMRI contrasts. Notably, using the Dunedin Study, we were able to predict participants cognitive abilities at ages 7, 9, and 11 using their multimodal MRI at age 45, with an out-of-sample r of 0.52. For test-retest reliability, stacked models reached an excellent level of reliability (ICC>.75), even when we stacked only task-fMRI contrasts together. For generalisability, a stacked model with non-task MRI built from one dataset significantly predicted cognitive abilities in other datasets. Altogether, stacking is a viable approach to undertake the three challenges of BWAS for cognitive abilities. Significance statementScientists have had limited success in predicting cognitive abilities from brain MRI. We proposed a machine learning method, called stacking, to draw information across different types of brain MRI. Using three large databases (n=2,131, 22-100 years old), we found stacking to make the prediction of cognitive abilities 1) closer to actual cognitive scores when applied to a new individual, not part of the modelling process, 2) reliable over times and 3) applicable to the data collected from different age groups and MRI scanners. Indeed, stacking, especially with fMRI task contrasts, allowed us to use MRI of people aged 45 to predict their childhood cognitive abilities reasonably well. Accordingly, stacking may help MRI realise its potential to predict cognitive abilities.

neuroscience↗

bioRxiv2024

Riluzole reverses blood-testis barrier loss to rescue chemotherapy induced male infertility by binding to TRPC

Cancer treatments, including cytotoxic therapy, often result in male infertility, necessitating the development of safe and effective strategies to preserve male reproductive potential during chemotherapy. Notably, our study uncovers the potential of repurposing riluzole, an FDA-approved drug for amyotrophic lateral sclerosis (ALS), in enhancing spermatogenesis. Hence, this research aims to explore the feasibility of utilizing riluzole to alleviate male infertility induced by busulfan (BSF), a commonly used chemotherapy drug. We established a BSF-induced oligospermia model in 4-week-old male mice and found that riluzole could effectively countered the detrimental effects of BSF on sperm production in mice with oligospermia. By restoring blood-testis barrier (BTB) functionality, riluzole improves sperm quality and reduces testicular atrophy. Through transcriptomic and molecular docking analyses, we identify transient receptor potential canonical subfamily member 5 (TRPC5) as a potential target for riluzole-mediated regulation of blood-testis barrier function. These findings propose riluzole as a promising therapeutic option for chemotherapy-induced male infertility, thereby addressing the fertility challenges associated with cancer treatments. Moreover, repurposing riluzole could streamline the drug development process, providing a cost-effective approach with reduced risk compared to developing entirely new drugs.

pharmacology and toxicology↗

bioRxiv2023

Spatially resolved molecular and cellular atlas of the mouse brain

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding function of the brain. Here, using snRNA-seq and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters with single-cell resolution involving over 6 million cells as well as for 29,655 genes. We have identified new astrocyte clusters, and demonstrated that distinct cell clusters exhibit preference for cortical subregions. In addition, we identified 155 genes exhibiting regional specificity in the brainstem, and 513 long non-coding RNA exhibited regional specificity in the adult brain. Parcellation of brain regions based on spatial transcriptomic information showed large overlap with that by traditional method. Furthermore, we have uncovered 411 transcription factor regulons with spatiotemporal specificity during development. Thus, our study has discovered genes and regulon with spatiotemporal specificity, and provided a high-resolution spatial transcriptomic atlas of the mouse brain.

neuroscience↗