ArticleProceedings of the National Academy of Sciences of the United States of America2010
Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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93 citing papers in PubMed, 152 citations in OpenAlex.
- Molecular evolution in light of regulatory-coding epistasis.EMBO reports · 2026Review
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- DNA Circles as Vehicles for Genes to Evade Chromosomal Discipline.Genome biology and evolution · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- Iterative SCRaMbLE for engineering synthetic genome modules and chromosomes.Nature communications · 2025Article
- Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress.Nature communications · 2025Article
- Molecular mechanisms of extrachromosomal circular DNA formation.Nucleic acids research · 2025Review
- Template switching during DNA replication is a prevalent source of adaptive gene amplification.eLife · 2025Article
- HapCNV: A Comprehensive Framework for CNV Detection in Low-input DNA Sequencing Data.bioRxiv : the preprint server for biology · 2025Article
- R-loops as a trigger for intra- and extrachromosomal DNA amplification in cancer.Frontiers in cell and developmental biology · 2025Review
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- Integrating Circle-Seq with transcriptomics reveals genome-wide characterization of extrachromosomal circular DNA for dilated cardiomyopathy.Biology direct · 2024Article
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- Template switching during DNA replication is a prevalent source of adaptive gene amplification.bioRxiv : the preprint server for biology · 2024Article
- Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies.Life (Basel, Switzerland) · 2024Review
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- Identification and characterization of extrachromosomal circular DNA in patients with high myopia and cataract.Epigenetics · 2023Article
- Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics.Cell genomics · 2023Article
33 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 4 institutions in 4 countries.
Funding
Abstract
To study adaptive evolution in defined environments, we performed evolution experiments with Saccharomyces cerevisiae (yeast) in nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated with adaptation and observed frequent amplifications and deletions at the GAP1 locus. GAP1 encodes the general amino acid permease, which transports amino acids across the plasma membrane. We identified a self-propagating extrachromosomal circular DNA molecule that results from intrachromosomal recombination between long terminal repeats (LTRs) flanking GAP1. Extrachromosomal DNA circles (GAP1(circle)) contain GAP1, the replication origin ARS1116, and a single hybrid LTR derived from recombination between the two flanking LTRs. Formation of the GAP1(circle) is associated with deletion of chromosomal GAP1 (gap1Δ) and production of a single hybrid LTR at the GAP1 chromosomal locus. The GAP1(circle) is selected following prolonged culturing in L-glutamine-limited chemostats in a manner analogous to the selection of oncogenes present on double minutes in human cancers. Clones carrying only the gap1Δ allele were selected under various non-amino acid nitrogen limitations including ammonium, urea, and allantoin limitation. Previous studies have shown that the rate of intrachromosomal recombination between tandem repeats is stimulated by transcription of the intervening sequence. The high level of GAP1 expression in nitrogen-limited chemostats suggests that the frequency of GAP1(circle) and gap1Δ generation may be increased under nitrogen-limiting conditions. We propose that this genomic architecture facilitates evolvability of S. cerevisiae populations exposed to variation in levels and sources of environmental nitrogen.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.