ArticleMicrobial genomics2018
Copy number variation is associated with gene expression change in archaea.
Article in Microbial genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- Archaea express circular isoforms of IS200/IS605-associated ωRNAs.Frontiers in microbiology · 2025Article
- Increased privatization of a public resource leads to spread of cooperation in a microbial population.Microbiology spectrum · 2024Article
- Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.Biomolecules · 2022Article
- Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics.PLoS biology · 2022Article
- A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH.Frontiers in microbiology · 2022Article
- Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon.Scientific reports · 2020Article
- Archaeal DNA Repair Mechanisms.Biomolecules · 2020Review
- Article
- Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs.eLife · 2020Article
- Gene Expression ofInternational journal of molecular sciences · 2019Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high-throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome. Some hotspots were strongly associated with changes in gene expression, suggesting a mechanism for phenotypic innovation. In contrast, CNV hotspots in other genomic loci left expression unchanged, suggesting buffering of certain phenotypes. The correspondence of CNVs with gene expression was validated with strain- and condition-matched transcriptomics and DNA quantification experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known insertion sequence (IS) elements suggested a mechanism for generating genomic instability. Given the efficient recombination capabilities in H. salinarum despite stability at the single nucleotide level, these results suggest that genomic plasticity mediated by IS element activity can provide a source of phenotypic innovation in extreme environments.
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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.