In reverse genetics, a gene's function is elucidated through targeted modifications in the coding region or associated DNA cis-regulatory elements. To this purpose, recently developed customizable transcription activator-like effector nucleases (TALENs) have proven an invaluable tool, allowing introduction of double-strand breaks at predetermined sites in the genome. Here we describe a practical and efficient method for the targeted genome engineering in Drosophila. We demonstrate TALEN-mediated targeted gene integration and efficient identification of mutant flies using a traceable marker phenotype. Furthermore, we developed an easy TALEN assembly (easyT) method relying on simultaneous reactions of DNA Bae I digestion and ligation, enabling construction of complete TALENs from a monomer unit library in a single day. Taken together, our strategy with easyT and TALEN-plasmid microinjection simplifies mutant generation and enables isolation of desired mutant fly lines in the F1 generation.
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http://dx.doi.org/10.1093/nar/gkt638 | DOI Listing |
Protoplasma
January 2025
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.
Stay-green (SG) and stem reserve mobilization (SRM) are two significant mutually exclusive traits, which contributes to grain-filling during drought and heat stress in wheat. The current research was conducted in a genome-wide association study (GWAS) panel consisting of 278 wheat genotypes of advanced breeding lines to find the markers linked with SG and SRM traits and also to screen the superior genotypes. SG and SRM traits, viz.
View Article and Find Full Text PDFSci China Life Sci
January 2025
State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits.
View Article and Find Full Text PDFBrief Bioinform
November 2024
School of Artificial Intelligence, Jilin University, 3003 Qianjin Street, 130012 Changchun, China.
Accurate identification of causal genes for cancer prognosis is critical for estimating disease progression and guiding treatment interventions. In this study, we propose CPCG (Cancer Prognosis's Causal Gene), a two-stage framework identifying gene sets causally associated with patient prognosis across diverse cancer types using transcriptomic data. Initially, an ensemble approach models gene expression's impact on survival with parametric and semiparametric hazard models.
View Article and Find Full Text PDFGenes Cells
January 2025
Department of Urology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
Tumor development often requires cellular adaptation to a unique, high metabolic state; however, the molecular mechanisms that drive such metabolic changes in TFE3-rearranged renal cell carcinoma (TFE3-RCC) remain poorly understood. TFE3-RCC, a rare subtype of RCC, is defined by the formation of chimeric proteins involving the transcription factor TFE3. In this study, we analyzed cell lines and genetically engineered mice, demonstrating that the expression of the chimeric protein PRCC-TFE3 induced a hypoxia-related signature by transcriptionally upregulating HIF1α and HIF2α.
View Article and Find Full Text PDFAdv Clin Exp Med
January 2025
Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, USA.
Background: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma (RCC). Due to the lack of symptoms until advanced stages, early diagnosis of ccRCC is challenging. Therefore, the identification of novel secreted biomarkers for the early detection of ccRCC is urgently needed.
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