Publications by authors named "Zhenxin Yan"

The differentiation of embryonic stem cells (ESCs) begins with the transition from the naive to the primed state. The formative state was recently established as a critical intermediate between the two states. Here, we demonstrate the role of the histone chaperone FACT in regulating the naive-to-formative transition.

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Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative disorders of the central nervous system (CNS). Increasing evidence supports the view that dysfunction of innate immune cells initiated by accumulated and misfolded proteins plays essential roles in the pathogenesis and progression of these diseases. The TLR family was found to be involved in the regulation of microglial function in the pathogenesis and progression of AD or PD, making it as double-edged sword in these diseases.

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Article Synopsis
  • Break-Induced Replication (BIR) is a unique pathway within homologous recombination that involves significant DNA synthesis during the G2/M phase of the cell cycle, unlike typical DNA replication.
  • This process starts with the invasion of a single end of a DNA double-strand break, and requires Pif1 helicase for extensive repair-specific DNA synthesis, while being independent of the main helicase Mcm2-7.
  • The study outlines methods to investigate BIR, focusing on identifying enzymes specific to this pathway, analyzing the effects of mutants lacking extensive synthesis, and tracking the DNA synthesis process using yeast models.
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Deoxythymidine diphospho-l-rhamnose (dTDP-l-rhamnose) is used by prokaryotic rhamnosyltransferases as the glycosyl donor for the synthesis of rhamnose-containing polysaccharides and compounds that have potential in pharmaceutical development, so its efficient synthesis has attracted much attention. In this study, we successfully cloned four putative dTDP-l-rhamnose synthesis genes from CGMCC 4.1716 and expressed them in .

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As a natural sweetening and solubilizing agent, rubusoside has great potential in the application of healthy beverages and pharmaceuticals. However, the direct extraction and purification of rubusoside from raw materials is inefficient. In this work, a novel β-glucosidase (BGL) was obtained from 1433 through screening of the environmental microorganisms.

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Single-stranded DNA (ssDNA) covered with the heterotrimeric Replication Protein A (RPA) complex is a central intermediate of DNA replication and repair. How RPA is regulated to ensure the fidelity of DNA replication and repair remains poorly understood. Yeast Rtt105 is an RPA-interacting protein required for RPA nuclear import and efficient ssDNA binding.

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Proton transfer from Brønsted acid sites (BASs) to alcohol molecules ignites the acid-catalyzed alcohol dehydration reactions. For aqueous phase dehydration reactions in zeolites, the coexisting water molecules around BASs in the zeolite pores significantly affect the alcohol dehydration activity. In the present work, proton transfer processes among the BASs of H-BEA zeolites, the adsorbed cyclohexanol and surrounding water clusters with different sizes up to 8 water molecules were investigated using ab initio molecular dynamics (AIMD) simulations combined with the multiple-walker well-tempered metadynamics algorithm.

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Article Synopsis
  • DNA synthesis during homologous recombination can cause mutations and template switches, with two types of DNA double-strand breaks (DSBs) being repaired differently: gene conversion for two-ended DSBs and break-induced replication (BIR) for single-ended DSBs.
  • Two-ended DSBs typically undergo limited mutagenic DNA synthesis, while BIR can lead to extensive DNA synthesis and mutations, though the mechanisms that suppress BIR at two-ended DSBs are not fully understood.
  • The study reveals that certain proteins, including Rad52, Rad59, Mph1, and the Mre11-Rad50-Xrs2 complex, work together to prevent BIR at two
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Break-induced replication (BIR) repairs one-ended double-strand breaks in DNA similar to those formed by replication collapse or telomere erosion, and it has been implicated in the initiation of genome instability in cancer and other human diseases. Previous studies have defined the enzymes that are required for BIR; however, understanding of initial and extended BIR synthesis, and of how the migrating D-loop proceeds through known replication roadblocks, has been precluded by technical limitations. Here we use a newly developed assay to show that BIR synthesis initiates soon after strand invasion and proceeds more slowly than S-phase replication.

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DNA double-strand break (DSB) end resection is an essential step for homologous recombination. It generates 3' single-stranded DNA needed for the loading of the strand exchange proteins and DNA damage checkpoint proteins. To study the mechanism of end resection in fission yeast, we apply a robust, quantitative and inducible assay.

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Hyperuricemia is characterized by abnormally high level of circulating uric acid in the blood and is associated with increased risk of kidney injury. The pathophysiological mechanisms leading to hyperuricemic nephropathy (HN) involve oxidative stress, endothelial dysfunction, inflammation, and fibrosis. Mangiferin is a bioactive C-glucoside xanthone, which has been exerting anti-inflammatory, anti-fibrotic, and antioxidative effects in many diseases.

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Hyperuricemia (HUA) is positively correlated with the progression of cardiovascular and metabolic diseases. Anti-HUA drugs aim to either reduce uric acid production or promote uric acid excretion. Urate transporter 1 (URAT1) is a major urate transporter involved in renal uric acid reabsorption and excretion, making it an important anti-HUA drug target.

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Article Synopsis
  • - Rad52 is essential for homologous recombination (HR) in yeast, aiding in the assembly of Rad51-ssDNA filaments and facilitating DNA annealing.
  • - Rad52 has a crucial pre-HR function that restricts the resection of DNA double-stranded break ends, which is needed to generate single-stranded DNA (ssDNA) tails.
  • - In studies with fission yeast, Rad52 regulates the activity of resection nucleases like Exo1 and Rqh1, controlling the resection rate and competing with Sgs1 to limit ssDNA production.
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Article Synopsis
  • Understanding genome plasticity benefits from assays that analyze recombination, repair, and mutagenesis, especially in microbial systems with easily manipulated genetic reporters.
  • These cellular assays include various types of reporters—genetic, molecular, and cytological—that help researchers study DNA processes.
  • The text reviews commonly used assays, highlighting their strengths and weaknesses, and offers guidelines for future research.
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Insertions of mobile elements, mitochondrial DNA and fragments of nuclear chromosomes at DNA double-strand breaks (DSBs) threaten genome integrity and are common in cancer. Insertions of chromosome fragments at V(D)J recombination loci can stimulate antibody diversification. The origin of insertions of chromosomal fragments and the mechanisms that prevent such insertions remain unknown.

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Non-homologous end joining (NHEJ) is a major pathway to repair DNA double-strand breaks (DSBs), which can display different types of broken ends. However, it is unclear how NHEJ factors organize to repair diverse types of DNA breaks. Here, through systematic analysis of the human NHEJ factor interactome, we identify PAXX as a direct interactor of Ku.

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Somatostatin receptors (SSTRs) are proposed to mediate the actions of somatostatin (SST) and its related peptide, cortistatin (CST), in vertebrates. However, the identity, functionality, and tissue expression of these receptors remain largely unknown in most non-mammalian vertebrates including birds. In this study, five SSTRs (named cSSTR1, cSSTR2, cSSTR3, cSSTR4, cSSTR5) were cloned from chicken brain by RT-PCR.

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IgD has been found in almost all jawed vertebrates, including cartilaginous and teleost fish. However, IgD is missing in acipenseriformes, a branch that is evolutionarily positioned between elasmobranchs and teleost fish. Here, by analyzing transcriptome data, we identified a transcriptionally active IgD-encoding gene in the Siberian sturgeon (Acipenser baerii).

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