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Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting.
Mol Syst Biol
December 2024
Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany.
Article Synopsis
- The study investigates how mRNA molecules move and are processed in different parts of mouse embryonic stem cells, measuring their rates of production, stability, and degradation.
- The researchers used a combination of techniques, including RNA labeling and sequencing, to analyze over 9,000 genes and found that many mature mRNAs have long lifetimes in the nucleus, suggesting that nuclear retention limits their overall flow.
- Additionally, the study reveals that mRNAs are regulated differently based on their location, with unique stability patterns for those associated with membranes and in the cytoplasm, providing insights into gene expression regulation across cellular compartments.
Concurrent Profiling of Localized Transcriptome and RNA Dynamics in Neurons by Spatial SLAMseq.
Methods Mol Biol
November 2024
Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
The asymmetric distribution of RNA within a cell plays a pivotal biological role, ensuring the distinctive shapes and functionality of subcellular compartments. In neurons, these mechanisms are fundamental to cellular growth, synaptic plasticity, and information processing. To understand these mechanisms, diverse methods have been developed to analyze localized transcripts.
View Article and Find Full Text PDFAssessment of mRNA Decay and Calculation of Codon Occurrence to mRNA Stability Correlation Coefficients after 5-EU Metabolic Labeling.
Methods Mol Biol
November 2024
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
mRNA translation and decay are tightly connected. This chapter describes a method to assess the influence of each codon identity on mRNA stability in cultured cells. The technique involves metabolic labeling of the nascent mRNAs by addition of the nucleoside analog 5-ethynyluridine (5-EU), purification of the RNA at different time-points after chase of the 5-EU, then biotinylation with Click chemistry, pull-down, and sequencing.
View Article and Find Full Text PDFPredicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.
Nat Commun
November 2024
Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its sequence, due to the many coupled interactions that control degradation rate. Here, we carried out massively parallel kinetic decay measurements on over 50,000 bacterial mRNAs, using a learn-by-design approach to develop and validate a predictive sequence-to-function model of mRNA stability. mRNAs were designed to systematically vary translation rates, secondary structures, sequence compositions, G-quadruplexes, i-motifs, and RppH activity, resulting in mRNA half-lives from about 20 seconds to 20 minutes.
View Article and Find Full Text PDFUnraveling RNA contribution to the molecular origins of bacterial surface-enhanced Raman spectroscopy (SERS) signals.
Sci Rep
August 2024
Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC.
Surface-enhanced Raman spectroscopy (SERS) is widely utilized in bacterial analyses, with the dominant SERS peaks attributed to purine metabolites released during sample preparation. Although adenosine triphosphate (ATP) and nucleic acids are potential molecular origins of these metabolites, research on their exact contributions remains limited. This study explored purine metabolite release from E.
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