Biology subjects

Shao, A.

Publications and source records attributed to Shao, A..

8 recordsLinked to original sources

bioRxiv2026

Hepatocyte nuclear factor-1β recruits the nucleosome remodeling and deacetylase complex to activate gene transcription

Mutations affecting the transcription factor hepatocyte nuclear factor-1{beta} (HNF-1{beta}) are the most common monogenic cause of congenital anomalies of the kidney and urinary tract. The mechanism whereby HNF-1{beta} regulates gene transcription remains unclear. Here, we performed an unbiased proteomic screen and found that endogenous HNF-1{beta} interacts with core subunits of the nucleosome remodeling and deacetylase complex (NuRD) in renal epithelial cells. Genome-wide ChIP-seq studies demonstrated colocalization of endogenous HNF-1{beta} and the core NuRD subunits GATAD2A, CHD4, and MBD3 at 2,776 primarily intergenic and intronic sites in native chromatin from wild-type renal epithelial cells. NuRD co-occupancy at 628 of the sites (22.6%) was reduced in the absence of HNF-1{beta}. Of the 628 HNF-1{beta}-dependent NuRD-occupied sites, 113 sites (18.2%) showed higher ATAC-seq peaks, indicative of open chromatin, and enrichment of histone H3 lysine-27 (H3K27) acetylation, indicative of active enhancers, in wild-type cells compared to HNF-1{beta}-deficient cells. Correlation with transcriptomic profiles in wild-type and HNF-1{beta}-deficient cells revealed that most of the sites were located near genes that are activated by HNF-1{beta}. Knockdown of CHD4 with shRNA resulted in decreased expression of 67 HNF-1{beta}-regulated genes that contained nearby NuRD and HNF-1{beta} co-occupied sites. Collectively, these results demonstrate that HNF-1{beta} recruits the NuRD complex resulting in H3K27 acetylation and chromatin opening and leading to gene activation. Our findings reveal a new mechanism of HNF-1{beta}-dependent gene expression and expand the role of the NuRD complex in gene activation at distal enhancers.

biochemistry↗

bioRxiv2026

Acute Toxicological Profile of Pharmaceutical-Grade Nicotinamide Riboside: A Route-Dependent Assessment Across Intravenous, Intramuscular, and Subcutaneous Administration

Nicotinamide riboside chloride (NR-Cl) has been studied predominantly by the oral route, while information regarding its toxicity following parenteral administration is limited. To characterize route-dependent acute toxicity and estimate median lethal doses (LD50), pharmaceutical-grade NR-Cl was evaluated following bolus intravenous (IV), intramuscular (IM), and subcutaneous (SC) administration in female Sprague Dawley rats, in three independent studies. All studies were conducted using an adapted OECD Guideline 425 Up-and-Down procedure, modified for parenteral administration, in the absence of standardized route-specific OECD guidance. Animals received a single dose of NR-Cl via the respective administration route and were monitored for mortality, clinical signs, bodyweight changes, and gross pathological findings over a 14-day observation period. Following IM and SC administration, no mortalities were observed at doses up to 2000 mg/kg, and LD50 values for both routes were determined to be greater than 2000 mg/kg. In contrast, IV administration yielded an estimated LD50 of approximately 2000 mg/kg. These findings demonstrate that the acute toxicity of NR-Cl differs by route of administration and establish foundational safety benchmarks to support future research.

pharmacology and toxicology↗

bioRxiv2024

Generative AI divide: How College Students' Backgrounds Affect Their Gen AI Literacy

In the field of education, generative artificial intelligence has a profound impact, mainly reflected in areas such as personalized learning, automated assignment evaluation, content generation, and open educational resources. However, some scholars have begun to discuss whether this technology may lead to new inequalities. Therefore, this study aims to explore how user background affects the performance of generative artificial intelligence technology through empirical research while focusing on the potential educational inequalities that may arise in the era of generative AI. The research found that generative artificial intelligence literacy is correlated with grade level, institutional tier, and academic discipline, with higher-grade students, those from prestigious universities, and those studying Applied Sciences and Natural Sciences demonstrating better performance.

scientific communication and education↗

bioRxiv2023

The L27 Domain of MPP7 enhances TAZ-YY1 Cooperation to Renew Muscle Stem Cells

Stem cells regenerate differentiated cells to maintain and repair tissues and organs. They also replenish themselves, i.e. self-renewal, for the regenerative process to last a lifetime. How stem cells renew is of critical biological and medical significance. Here we use the skeletal muscle stem cell (MuSC) to study this process. Using a combination of genetic, molecular, and biochemical approaches, we show that MPP7, AMOT, and TAZ/YAP form a complex that activates a common set of target genes. Among these targets, Carm1 can direct MuSC renewal. In the absence of MPP7, TAZ can support regenerative progenitors and activate Carm1 expression, but not to a level needed for self-renewal. Facilitated by the actin polymerization-responsive AMOT, TAZ recruits the L27 domain of MPP7 to up-regulate Carm1 to the level necessary to drive MuSC renewal. The promoter of Carm1, and those of other common downstream genes, also contain binding site(s) for YY1. We further demonstrate that the L27 domain of MPP7 enhances the interaction between TAZ and YY1 to activate Carm1. Our results define a renewal transcriptional program embedded within the progenitor program, by selectively up-regulating key gene(s) within the latter, through the combination of protein interactions and in a manner dependent on the promoter context.

developmental biology↗

bioRxiv2023

GET: a foundation model of transcription across human cell types

Transcriptional regulation, involving the complex interplay between regulatory sequences and proteins, directs all biological processes. Computational models of transcription lack generalizability to accurately extrapolate in unseen cell types and conditions. Here, we introduce GET, an interpretable foundation model designed to uncover regulatory grammars across 213 human fetal and adult cell types. Relying exclusively on chromatin accessibility data and sequence information, GET achieves experimental-level accuracy in predicting gene expression even in previously unseen cell types. GET showcases remarkable adaptability across new sequencing platforms and assays, enabling regulatory inference across a broad range of cell types and conditions, and uncovering universal and cell type specific transcription factor interaction networks. We evaluated its performance on prediction of regulatory activity, inference of regulatory elements and regulators, and identification of physical interactions between transcription factors. Specifically, we show GET outperforms current models in predicting lentivirus-based massive parallel reporter assay readout with reduced input data. In fetal erythroblasts, we identify distal (>1Mbp) regulatory regions that were missed by previous models. In B cells, we identified a lymphocyte-specific transcription factor-transcription factor interaction that explains the functional significance of a leukemia-risk predisposing germline mutation. In sum, we provide a generalizable and accurate model for transcription together with catalogs of gene regulation and transcription factor interactions, all with cell type specificity.

bioinformatics↗

bioRxiv2021

Arap1 Loss Causes RPE Phagocytic Dysfunction and Subsequent Photoreceptor Death

PurposeArap1 is an Arf-directed GTPase-activating protein (GAP) shown to modulate actin cytoskeletal dynamics by regulating Arf and Rho family members. We have previously shown that Arap1-/- mice develop photoreceptor degeneration similar to the human condition retinitis pigmentosa (RP), corroborated by fundus examination, histopathology, and ERG analysis. However, Arap1 expression was not detected in photoreceptors, but in Muller Glia and retinal pigment epithelium (RPE), suggesting a non-cell-autonomous mechanism for degeneration. The aim of this study was to elucidate the role of retinal Arap1 in photoreceptor maintenance. MethodsAlbino Arap1-/- mice were generated via breeding pigmented Arap1-/- mice onto a Tyr-/- C57BL/6J background. Conditional knockout (cKO) mice were generated for Muller Glia/RPE, Muller Glia, and RPE via targeting Cralbp, Glast, and Vmd2 promoters, respectively, to drive Cre recombinase expression to knock out Arap1. Mice were analyzed by fundus photography, optical coherence tomography (OCT), histology, and immunohistochemistry. Arap1 binding partners were assayed by affinity purification mass spectrometry. ResultsVmd2-Cre Arap1tm1c/tm1c and Cralbp-Cre Arap1tm1c/tm1c mice, but not Glast-Cre Arap1tm1c/tm1c mice, recapitulated the photoreceptor degeneration phenotype originally observed in germline Arap1-/- mice. These findings were corroborated by fundus exam, OCT, and histological analysis. Mass spectrometry analysis of ARAP1 co-immunoprecipitation identified putative binding partners of ARAP1, revealing numerous interactants involved in phagocytosis, cytoskeletal composition, intracellular trafficking, and endocytosis. Quantification of rod outer segment (OS) phagocytosis in vivo demonstrated a clear phagocytic defect in Arap1-/- mice compared to Arap1+/+ littermate controls while cone phagocytosis was preserved. ConclusionsArap1 expression, specifically in RPE, is necessary for photoreceptor survival due to its indispensable function in RPE phagocytosis. We propose a model in which Arap1 regulates G-protein function for nonmuscle myosin II targeting during phagocytosis. This novel role of Arap1 is important for further understanding of both the diversity of its functions and the complex molecular regulation of RPE phagocytosis.

molecular biology↗

bioRxiv2020

Intein-assisted bisection mapping systematically splits proteins for Boolean logic and inducibility engineering

Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augmented a mini-Mu transposon-based screening approach and devised the intein-assisted bisection mapping (IBM) method. IBM robustly revealed clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further showed that the use of inteins expands functional sequence space for splitting a protein. We also demonstrated the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins. Furthermore, the intein inserted at an identified site could be engineered by the transposon again to become partially chemically inducible, and to some extent enabled post-translational tuning on host protein function. Our work offers a generalizable and systematic route towards creating split protein-intein fusions and conditional inteins for protein activity control.

synthetic biology↗

bioRxiv2019

Facilitators and Barriers to Linkage to HIV Care and Treatment among Female Sex Workers in a Community-based HIV Prevention Intervention in Tanzania: a qualitative study

BackgroundHIV-infected female sex workers (FSWs) have poor linkage to HIV care in sub-Sahara Africa.\n\nMethodsWe conducted 21 focus group discussions (FGDs) to explore factors influencing linkage to HIV care among FSWs tested for HIV through a comprehensive community-based HIV prevention project in Tanzania.\n\nResultsInfluences on linkage to care were present at the system, societal and individual levels. System-level factors included unfriendly service delivery environment, including lengthy pre-enrolment sessions, concerns about confidentiality, stigmatising attitudes of health providers. Societal-level factors included myths and misconceptions about ART and stigma. On the individual level, most notable was fear of not being able to continue to have a livelihood if ones status were to be known. Facilitators were noted, including the availability of transport to services, friendly health care providers and peer-support referral and networks.\n\nConclusionFindings of this study underscore the importance of peer-supported linkages to HIV care and the need for respectful, high-quality care.

epidemiology↗