395: Extended sequence context shapes mutational bias in Escherichia coli

Green R et al., PNAS - Collating >100,000 base-pair substitutions from 32 mutation-accumulation experiments, this study shows that sequence context well beyond adjacent bases — up to ±6 bp and even hundreds of bp — shapes mutational biases in E. coli and interacts with DNA repair. Key terms: mutational bias, sequence context, Escherichia coli, mismatch repair, mononucleotide runs. Study Highlights: The authors analyzed 117,807 base-pair substitutions from 32 MA experiments and quantified nucleotide frequencies up to ±6 bp (and sliding windows to 1,000 bp) around mutation sites. Extended context effects vary by substitution type, DNA repair background (proofreading and MMR), and replication strand. Mononucleotide runs (notably AC3+ and GC3+) are strong hotspots consistent with transient misalignment; GC3+ can increase G:C→C:G transversions by orders of magnitude. Broader GC% biases persist hundreds of base pairs and are modulated by MMR activity. Conclusion: Extended sequence context and its interaction with proofreading, mismatch repair, and replication strand identity create complex, BPS-specific mutational signatures in E. coli, improving the resolution of mutation-rate predictions and highlighting long-range and motif-specific hotspots. Music: Enjoy the music based on this article at the end of the episode. Article title: Extended sequence context shapes mutational bias in Escherichia coli First author: Green R Journal: PNAS DOI: 10.1073/pnas.2601345123 Reference: Green R., Jago M.J., Knight C.G., Czernuszka M.R., Denisova S., Krašovec R., Lagator M. Extended sequence context shapes mutational bias in Escherichia coli. PNAS. 2026;123(23):e2601345123. doi:10.1073/pnas.2601345123. License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/extended-sequence-context-mutational-bias-e-coli QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-06-18. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited sections covering extended sequence context (±6 bp), mononucleotide run hotspots (AC3+, GC3+), GC3+ and G:C→C:G transversions, 5′ preceding nucleotide effects, leading vs lagging strand replication, and GC-content effects up to 1000 bp. - transcript topics: Extended sequence context (±6 bp); Mononucleotide runs and transient misalignment; GC3+ hotspot and other motifs; DNA proofreading and mismatch repair effects; Leading vs lagging strand replication and context biases; Regional GC-content effects up to 1000 bp QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 6 - claims flagged for review: 0 - metadata checks passed: 4 - metadata issues found: 0 Metadata Audited: - article_doi - article_title - article_journal - license Factual Items Audited: - Extended context up to ±6 bp influences mutational bias beyond trinucleotide context - Mononucleotide runs AC3+ and GC3+ are mutational hotspots; GC3+ increases G:C→C:G transversions up to ~10^4-fold - A strong GC3+ hotspot near GG sequences can reach extremely large fold increases; in some backgrounds ~50,000-fold for G:C→C:G transversions at GG C7 - 5′ preceding nucleotide...