Transcription Factor Lbx1 Expression in Mouse Embryonic Stem Cell-Derived Phenotypes by Stefanie Schmitteckert, Cornelia Ziegler, Liane Kartes, Alexandra Rolletschek

“…During in vitro differentiation, ES cells recapitulate cellular developmental processes and gene expression patterns of early embryogenesis. …”
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Protocol for profiling RNA m5C methylation at base resolution using m5C-TAC-seq by Xiaoting Zhang, Liang Lu, Chengqi Yi, Xiaoyu Li

“…Summary: RNA 5-methylcytosine (m5C) is a widespread modification and plays a crucial role in gene expression regulation. Here, we present a protocol for transcriptome-wide m5C methylome profiling at base resolution using bisulfite-free m5C detection strategy enabled by ten-eleven translocation (TET)-assisted chemical labeling sequencing (m5C-TAC-seq). …”
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The Effects of MicroRNAs on Key Signalling Pathways and Epigenetic Modification in Fibroblast-Like Synoviocytes of Rheumatoid Arthritis by Wenming Hong, Pengying Zhang, Xinming Wang, Jiajie Tu, Wei Wei

“…MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level via direct binding to the 3′-untranslated region (UTR) of target mRNAs. …”
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Identification of Molecular Subtypes and Prognostic Features of Breast Cancer Based on TGF-β Signaling-related Genes by Jia Qu, Mei-Huan Wang, Yue-Hua Gao, Hua-Wei Zhang

“…The GSE161529 dataset from the Gene Expression Omnibus was employed to conduct single-cell analyses aimed at further elucidating the characteristics of these TSRGs. …”
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Organoid development and applications in gynecological cancers: the new stage of tumor treatment by Yang Li, Meiying Qin, Ning Liu, Chunmei Zhang

“…In contrast to traditional cell lines and patient-derived xenograft (PDX) models, gynecologic cancer organoids accurately mirror the genetic mutations and specific gene expression profiles of primary tumors. This review provides an overview of recent advancements in the development of gynecologic cancer organoid models, highlighting their contributions to understanding disease mechanisms, facilitating drug discovery, and advancing precision medicine. …”
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The Role of Plant DNA Methylation in Development, Stress Response, and Crop Breeding by Shuai Qiao, Wei Song, Wentao Hu, Fang Wang, Anzhong Liao, Wenfang Tan, Songtao Yang

“…We explore how these elements function within the broader epigenetic framework, focusing on their contributions to silencing transposable elements, modulating gene expression, and shaping chromatin architecture. The review also examines the significance of DNA methylation in plant development, particularly its role in adapting to biotic and abiotic stresses. …”
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Spatiotemporal Pattern of Neuroinflammation After Impact-Acceleration Closed Head Injury in the Rat by Servan Rooker, Sebastian Jander, Jos Van Reempts, Guido Stoll, Philippe G. Jorens, Marcel Borgers, Jan Verlooy

“…Our study shows rapid induction of inflammatory gene expression that exceeds by far the primary impact site and might therefore contribute to tissue damage at remote sites.…”
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Feature selection in single-cell RNA sequencing data: a comprehensive evaluation by Petros Paplomatas, Konstantinos Lazaros, Georgios N. Dimitrakopoulos, Aristidis Vrahatis

“…Unlike bulk RNA sequencing, scRNA-seq allows for examining gene expression at the individual cell level, revealing cellular heterogeneity and identifying rare cell types. …”
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Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data by Jinming Cheng, Xinyi Jin, Gordon K. Smyth, Yunshun Chen

“…Abstract Background Imaging-based spatial transcriptomics technologies allow us to explore spatial gene expression profiles at the cellular level. Cell type annotation of imaging-based spatial data is challenging due to the small gene panel, but it is a crucial step for downstream analyses. …”
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Control of Cellular Differentiation Trajectories for Cancer Reversion by Jeong‐Ryeol Gong, Chun‐Kyung Lee, Hoon‐Min Kim, Juhee Kim, Jaeog Jeon, Sunmin Park, Kwang‐Hyun Cho

“…Abstract Cellular differentiation is controlled by intricate layers of gene regulation, involving the modulation of gene expression by various transcriptional regulators. …”
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Identification of CDKN3 overexpression as a marker of poor prognosis and potential therapeutic target in low-grade glioma by Hongbing Cheng, Xiao Meng, Yanhua Zhang, Pu Wang, Yucheng Lu

“…The results showed that high CDKN3 expression in LGG patients was significantly associated with poor survival outcomes. Further gene expression analysis revealed that 379 genes were significantly upregulated in LGG samples with high CDKN3 expression, and these genes were primarily involved in the mitotic cell cycle and extracellular matrix organization. …”
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Chemo-selective modification of cysteine residue: synthesis and application in the discovery of potential drug candidates by Yanyan Liao, Xuefeng Jiang

“…Cysteine (Cys), one of the less abundant AAs in many biological proteins, plays a vital role in the catalysis, signal transduction, and redox regulation of gene expression. In natural AAs (α-AAs) residues, Cys exhibits high nucleophilicity and low redox-active potential, making it a primary target for site-selective conjugation. …”
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Genome-wide association study and candidate gene identification for the cold tolerance at the seedling stage of rapeseed (Brassica napus L.) by Guangyu Wu, Yanda Zhou, Jingyi Zhang, Mengjie Gong, Lixi Jiang, Yang Zhu

“…These results suggested that variation in the genomic sequences of BnaA8.MYB60 caused the divergence of gene expression levels and functions on cold tolerance in rapeseed seedlings. …”
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MicroRNA-Regulated Proinflammatory Cytokines in Sarcopenia by Jingjing Fan, Xianjuan Kou, Yi Yang, Ning Chen

“…MicroRNAs (miRNAs) have emerged as the important regulators for the mass and functional maintenance of skeletal muscle through regulating gene expression of proinflammatory cytokines. In this paper, we have systematically discussed regulatory mechanisms of miRNAs for the expression and secretion of inflammatory cytokines during sarcopenia, which will provide some novel targets and therapeutic strategies for controlling aging-related atrophy of skeletal muscle and corresponding chronic inflammatory diseases.…”
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Methylation Marks of Blood Leukocytes of Native Hucul Mares Differentiated in Age by T. Ząbek, E. Semik-Gurgul, T. Szmatoła, A. Gurgul, A. Fornal, M. Bugno-Poniewierska

“…A positive correlation was found between methylation states and gene expression in particular loci from our data set. …”
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The role of DNA methylation in the disorders of bone metabolism by B. I. Yalaev, A. V. Tyurin, R. Y. Mirgalieva, R. I. Khusainova

“…It is possible that DNA methylation is one of these links and a mechanism for epigenetic regulation of gene expression. Evidence exists that this mechanism alongside regulatory miRNAs and post-translational modifications makes a significant contribution to the central processes of bone remodeling; however, the results of various studies vary greatly, and, therefore, there is a need to understand the significance of the accumulated data and to make them consistent. …”
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Key Roles of p53 Signaling Pathway-Related Factors GADD45B and SERPINE1 in the Occurrence and Development of Gastric Cancer by Yaoqing Li, Liyijing Shen, Kelong Tao, Guangen Xu, Kewei Ji

“…We tried to identify the key factors of the p53 signaling pathway involved in gastric cancer (GC) occurrence and development based on the genotype-tissue expression (GTEx) and the Cancer Genome Atlas (TCGA) screening. We downloaded gene expression data and clinical data of GC included in the GTEx and TCGA databases, followed by differential analysis. …”
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Functionally-informed fine-mapping identifies genetic variants linking increased CHD1L expression and HIV restriction in monocytes by Riley H. Tough, Paul J. McLaren, The International Collaboration for the Genomics of HIV

“…However, it remains unclear if HIV spVL associated variants are associated with CHD1L gene expression changes. Here we apply a heuristic fine-mapping approach to prioritize combinations of variants that explain the majority of set-point viral load variance and identify variants likely driving the association. …”
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Mouse Reporter Strain for Noninvasive Bioluminescent Imaging of Cells that have Undergone Cre-Mediated Recombination by Michal Safran, William Y. Kim, Andrew L. Kung, James W. Horner, Ron A. DePinho, William G. Kaelin

“…Conditional alleles containing LoxP recombination sites, in conjunction with Cre recombinase delivered by a variety of means, allows for spatial and temporal control of gene expression in mouse models. Here we describe a mouse strain in which a luciferase (Luc) cDNA, preceded by a LoxP-stop-LoxP (L-S-L) cassette, was introduced into the ubiquitously expressed ROSA26 locus. …”
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Apiospora arundinis, a panoply of carbohydrate-active enzymes and secondary metabolites by Trine Sørensen, Celine Petersen, Asmus T. Muurmann, Johan V. Christiansen, Mathias L. Brundtø, Christina K. Overgaard, Anders T. Boysen, Rasmus D. Wollenberg, Thomas O. Larsen, Jens L. Sørensen, Kåre L. Nielsen, Teis E. Sondergaard

“…Through transcriptomic analysis, we observed differential gene expression in response to varying growth media, with several genes related to carbohydrate metabolism showing significant upregulation when the fungus was cultivated on a hay-based medium. …”
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