ArticleNature microbiology2022
Chromosome organization affects genome evolution in Sulfolobus archaea.
Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 37 citations in OpenAlex.
- Profiling large-scale protein occupancy on bacterial genomes using IPOD-HR.Nature protocols · 2026Review
- Review
- Sulfolobales: Acidothermophilic archaea as models for biology and biotechnological applications.Engineering microbiology · 2026Review
- Successive waves of transcriptional repression and de-repression license cell cycle progression in an archaeon.Nucleic acids research · 2026Article
- High-Resolution Chromosome Conformation Capture Method to Study Archaeal SMC Complexes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- On the origins and variation of nucleotide skews of archaeal genomes.Frontiers in microbiology · 2026Article
- The Lrs14-Like AbfR1 Homolog From Metallosphaera sedula Is a Nucleoid-Organizing Protein.MicrobiologyOpen · 2025Article
- Transcriptional landscape of the cell cycle in a model thermoacidophilic archaeon reveals similarities to eukaryotes.Nature communications · 2025Article
- Chromatin and gene regulation in archaea.Molecular microbiology · 2025Review
- Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure.Nature communications · 2025Article
- Capturing chromosome conformation in Crenarchaea.Molecular microbiology · 2025Review
- The chromatin landscape of the histone-possessingGenome research · 2025Article
- Nanopore sequencing reveals that DNA replication compartmentalisation dictates genome stability and instability in Trypanosoma brucei.Nature communications · 2025Article
- Hi-C/3C-seq Data Analysis for Prokaryotic Genomes with HiC-Pro.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Long range segmentation of prokaryotic genomes by gene age and functionality.Nucleic acids research · 2024Article
- Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS.Nucleic acids research · 2024Article
- Long range segmentation of prokaryotic genomes by gene age and functionality.bioRxiv : the preprint server for biology · 2024Article
- Article
- How Do Thermophiles Organize Their Genomes?Microbes and environments · 2024Review
- Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins.Nature microbiology · 2024Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.
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