研究目的
To investigate the localization and dynamics of mRNAs in stress granules and P-bodies during the integrated stress response and its effects on translation and degradation.
研究成果
mRNAs are dynamically localized to SGs and PBs during stress, with specific cis-elements and trans-factors like LARP1 influencing this. Granule localization does not affect mRNA translation or degradation rates during recovery, challenging the notion of granules as active sorting sites. Provides a single-molecule framework for studying phase-separated compartments.
研究不足
The study focuses on sodium arsenite-induced stress; other stressors or disease-related granules may yield different results. The low frequency of mRNA movement between SGs and PBs limits conclusions on active sorting. Overexpression of markers might affect granule properties.
1:Experimental Design and Method Selection:
Used single-molecule imaging in living human cells to monitor mRNA localization to SGs and PBs during sodium arsenite-induced stress. Engineered HeLa cell lines with fluorescent markers for SGs (G3BP1-GFP), PBs (TagRFP-T-DDX6), and mRNAs (NLS-MCP-Halo bound to MS2 stem loops).
2:Sample Selection and Data Sources:
HeLa cells were used as the model system. Three mRNA reporters were designed: Renilla luciferase, 5' TOP Renilla (with RPL32 5' UTR), and Gaussia luciferase (ER-associated). Cells were treated with 100 μM sodium arsenite to induce stress.
3:List of Experimental Equipment and Materials:
Microscopes (Zeiss Axioimager Z1, Nikon Eclipse Ti-E with HILO setup), fluorescent proteins (GFP, TagRFP-T, Halo ligands JF549/JF646), antibodies (anti-G3BP1, anti-DDX6, anti-LARP1), siRNAs for knockdown, and various chemicals (sodium arsenite, doxycycline).
4:Experimental Procedures and Operational Workflow:
Cells were induced with doxycycline, treated with sodium arsenite, and imaged over time. Single-molecule tracking, smFISH, immunofluorescence, and western blotting were performed. Data analyzed using Fiji, TrackMate, KNIME, and custom MATLAB scripts.
5:Data Analysis Methods:
Quantified mRNA colocalization with granules, movement dynamics, translation rates (using SunTag system), and degradation rates (using TREAT assay). Statistical analysis with Student's t-test.
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microscope
Axioimager Z1
Zeiss
Imaging fixed cells for smFISH and immunofluorescence
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laser
iBEAM SMART
Toptica
Excitation light source for imaging
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laser
Sapphire
Coherent
Excitation light source for imaging
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microscope
Eclipse Ti-E
Nikon
Live-cell imaging with HILO setup
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camera
Evolve 512 Delta
Photometrics
EMCCD camera for detecting fluorescence
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software
Fiji
Open Source
Image processing and analysis
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software
TrackMate
Fiji Plugin
Single-particle tracking
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software
KNIME
KNIME AG
Data analysis and workflow management
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software
AIRLOCALIZE
MATLAB
Spot detection in images
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dye
JF549
Janelia Fluor
Fluorescent labeling of HaloTag proteins
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dye
JF646
Janelia Fluor
Fluorescent labeling of HaloTag proteins
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antibody
anti-G3BP1
Aviva Systems Biology
Immunofluorescence staining for stress granules
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antibody
anti-DDX6
Bethyl Labs
Immunofluorescence staining for P-bodies
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siRNA
LARP1 siRNA
GE Dharmacon
Knockdown of LARP1 protein
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