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Updated: Feb 23, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic
1Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Site Jacques Monod, Lyon, France.
Cellular processes like RNA and protein synthesis pose risks to DNA stability, potentially leading to toxic aggregates. This review suggests that genetic variations arise to alleviate these constraints, driven by small RNAs and impacting genome evolution.
Area of Science:
- Molecular Biology
- Genetics
- Biophysics
Background:
- RNA and protein biogenesis can destabilize DNA and form toxic aggregates.
- Physicochemical properties of nascent molecules challenge cellular integrity.
Purpose of the Study:
- To explore how co-transcriptional and co-translational constraints influence DNA instability.
- To investigate the role of small RNAs in directed genetic variation and genome evolution.
Main Methods:
- Literature review of molecular pathways and biophysical constraints.
- Analysis of gene expression, DNA stability, and small RNA biogenesis.
Main Results:
- Biophysical constraints during transcription/translation can induce DNA instability.
- This instability favors the emergence of DNA sequences that reduce such constraints.
- Small RNAs transcribed from challenged DNA regions can increase local mutation rates.
Conclusions:
- Gene expression-related biophysical constraints act as a driving force in genome evolution.
- A mechanism involving small RNAs and anti-parasite defense pathways is proposed.
- Cellular biogenesis processes are linked to directed genome evolution.
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