Protective effect of silencing lncRNA HCP5 against brain injury after intracerebral hemorrhage by targeting miR-195-5p

BMC Neuroscience, Год журнала: 2025, Номер 26(1)

Опубликована: Янв. 8, 2025

Intracerebral hemorrhage (ICH) is a common subtype of stroke, characterized by high mortality rate and tendency to cause neurological damage. This study aims investigate the role mechanisms lncRNA HCP5 in ICH. We simulated ICH vivo injecting collagenase into rats established an vitro model using hemoglobin-treated BV2 cells. miR-195-5p levels were quantified RT-qPCR. mNSS score was used evaluate deficits rats. The dry-wet weight method assessed degree brain edema. Cell viability apoptosis rates determined CCK-8 assay flow cytometry, respectively. targeting relationship between confirmed dual-luciferase reporter assays RNA immunoprecipitation. ELISA utilized measure inflammatory factors, commercial kits detect MDA ROS levels. In rats, significantly elevated. It also found that silencing alleviated edema there marked improvement ICH-induced neuroinflammation oxidative stress. Moreover, sponge miR-195-5p, inhibiting could counteract neuroprotective effects HCP5. Similar results obtained experiments with Silencing can alleviate edema, dysfunction, neuroinflammation, stress caused via miR-195-5p.

Язык: Английский

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Single-Cell Transcriptomics Applied in Plants

Cells, Год журнала: 2024, Номер 13(18), С. 1561 - 1561

Опубликована: Сен. 17, 2024

Single-cell RNA sequencing (scRNA-seq) is a high-tech method for characterizing the expression patterns of heterogeneous cells in same tissue and has changed our evaluation biological systems by increasing number individual analyzed. However, full potential scRNA-seq, particularly plant science, not yet been elucidated. To explore utilization scRNA-seq technology plants, we firstly conducted comprehensive review significant findings past few years. Secondly, introduced research applications to tissues recent years, primarily focusing on model crops, wood. We then offered five databases that could facilitate identification distinct marker genes various cell types. Finally, analyzed problems, challenges, directions applying with aim providing theoretical foundation better use this technique future research.

Язык: Английский

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An overview of single-cell high-throughput technology in plants

Elsevier eBooks, Год журнала: 2025, Номер unknown, С. 1 - 34

Опубликована: Янв. 1, 2025

Язык: Английский

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Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer

Non-Coding RNA, Год журнала: 2025, Номер 11(2), С. 24 - 24

Опубликована: Март 10, 2025

Non-coding RNAs (ncRNAs) play crucial roles in colorectal cancer (CRC) development and progression. Recent developments single-cell transcriptome profiling methods have revealed surprising levels of expression variability among seemingly homogeneous cells, suggesting the existence many more cell types than previously estimated. This review synthesizes recent advances ncRNA research CRC, emphasizing bioinformatics approaches for their analysis. We explore computational tools used identification, characterization, functional prediction with a focus on RNA sequencing (scRNA-seq) data. The highlights key strategies, including sequence-based structure-based approaches, machine learning applications, multi-omics data integration. discuss how these techniques can be applied to analyze differential expression, perform enrichment, construct regulatory networks involving ncRNAs CRC. Additionally, we examine role leveraging as diagnostic prognostic biomarkers also scRNA-seq studies revealing heterogeneity aims provide comprehensive overview current state CRC outline future directions this rapidly evolving field, integration experimental validation advance our understanding biology

Язык: Английский

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A large-scale gene co-expression network analysis reveals Glutamate Dehydrogenase 2 (GhGDH2_D03) as a hub regulator of salt and salt-alkali tolerance in cotton

Plant Molecular Biology, Год журнала: 2025, Номер 115(2)

Опубликована: Апрель 1, 2025

Язык: Английский

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Multidimensional analysis of long noncoding RNAs function in Solanaceae plants

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Июнь 1, 2025

Summary Long noncoding RNAs (lncRNAs) have been gradually verified as functional regulators in plants, yet their functions remain underexplored, especially the Solanaceae family. While substantial progress has made identifying lncRNAs different species, systematic annotations are lacking. In this study, we uniformly identified and systematically characterized from seven Solanaceous species using large‐scale strand‐specific RNA‐seq (ssRNA‐seq). About 113 700 lncRNA genes were obtained analyzed for sequence, conservation, expression profile, epigenetic signals, genetic mutants. tomato, 97.4% of annotated with basic characteristics. Also, 25.7% further predicted to be involved stress response, development, metabolism. Comparisons between protein‐coding (PCGs) highlighted unique characteristics tissue expression, responses, sequence composition, signal distribution. We shared our datasets on at http://solanaceae‐lncrna‐source.liu‐lab.com/ . Taking fruit development ripening an example, mined data resources a total 1158 associated process, presenting how curated can utilized discover plant lncRNAs. Overall, study provides comprehensive multidimensional framework research, which serves valuable reference understanding other plants.

Язык: Английский

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Uncovering functional lncRNAs by scRNA-seq with ELATUS

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Ноя. 9, 2024

Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study single-cell (sc) level is challenging due to less accurate annotation low compared protein-coding genes. Here, we systematically benchmark different preprocessing methods develop a computational framework, named ELATUS, based on the combination of pseudoaligner Kallisto with selective functional filtering. ELATUS enhances detection lncRNAs from scRNA-seq data, detecting higher concordance than standard ATAC-seq profiles multiome data. Interestingly, better results are its advanced performance an inaccurate reference such as that lncRNAs. We independently confirm patterns type-specific exclusively detected unveil biologically important lncRNAs, AL121895.1, previously undocumented cis-repressor lncRNA, whose role breast cancer progression unnoticed by traditional methodologies. Our emphasize necessity for alternative workflow tailored sheds light multifaceted

Язык: Английский

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Manual correction of genome annotation improved alternative splicing identification of Artemisia annua

Planta, Год журнала: 2023, Номер 258(4)

Опубликована: Сен. 18, 2023

Язык: Английский

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Gene regulatory networks in abiotic stress responses via single-cell sequencing and spatial technologies: Advances and opportunities

Current Opinion in Plant Biology, Год журнала: 2024, Номер 82, С. 102662 - 102662

Опубликована: Ноя. 13, 2024

Язык: Английский

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Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 9, 2024

ABSTRACT Single-molecule fluorescence in situ hybridization (smFISH) has emerged as a powerful tool to study gene expression dynamics with unparalleled precision and spatial resolution variety of biological systems. Recent advancements have expanded its application encompass plant studies, yet demand persists for simple robust smFISH method adapted tissue sections. Here, we present an optimized protocol (cryo-smFISH) visualizing quantifying single mRNA molecules cryosections. This exhibits remarkable sensitivity, capable detecting low-expression transcripts, including long non-coding RNAs. Integrating deep learning-based algorithm our image analysis pipeline, enables us assign RNA abundance precisely nuclear cytoplasmic compartments. Compatibility Immunofluorescence also allows endogenous proteins be visualized quantified simultaneously. Finally, this presents the first time use single-cell sequencing (scRNA-seq) validation plants. By extending cryosections, even broader community scientists will able exploit multiple potentials quantitative transcript at cellular subcellular resolutions.

Язык: Английский

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