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Updated: Jan 16, 2026
08:34
MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
Published on: February 23, 2021
7.5K
Transcriptome-wide analysis reveals sequence selection to avoid mRNA aggregation in E. coli
Marco Todisco1, Ankur Jain1,2
1Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.
Biorxiv : the Preprint Server for Biology
|September 26, 2025
Summary
RNA
Area of Science:
- Molecular Biology
- Genomics
- Biophysics
Background:
- RNA base pairing and its limited code can lead to promiscuous interactions.
- In vitro, these interactions cause RNA self-assembly into aggregates.
Purpose of the Study:
- To determine the extent of RNA aggregation driven by sequence-encoded chemistry alone within a cellular environment.
- To investigate the role of evolutionary selection in maintaining transcriptome solubility.
Main Methods:
- Large-scale kinetic simulations of the Escherichia coli transcriptome.
- Evolutionary analysis of native E. coli sequences compared to controls.
Main Results:
- Sequence-encoded base-pairing energetics can generate dynamic networks of large RNA aggregates.
- Native E. coli sequences show selection against aggregation: more stable folding, fewer unstructured regions, and weaker intermolecular contacts.
- Dinucleotide-preserving controls exhibit increased aggregation propensity.
Conclusions:
- Maintaining transcriptome solubility is a significant evolutionary constraint on genome evolution.
- Cellular RNA management strategies may have evolved to counteract inherent aggregation tendencies.
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