ArticleNucleic acids research2017
Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 22 citations in OpenAlex.
- Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress.Nature communications · 2024Article
- The jet-like chromatin structure defines active secondary metabolism in fungi.Nucleic acids research · 2024Article
- Nuclear genome organization in fungi: from gene folding to Rabl chromosomes.FEMS microbiology reviews · 2023Article
- Spatial Organization of Gene Expression in Systems of Cellular Differentiation and Autoimmune Diseases.Advances in experimental medicine and biology · 2023Article
- Distinct chromosomal "niches" in the genome ofNAR genomics and bioinformatics · 2022Article
- G1/S transcription factors assemble in increasing numbers of discrete clusters through G1 phase.The Journal of cell biology · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Monitoring the prolonged Tnf stimulation in space and time with topological-functional networks.Computational and structural biotechnology journal · 2020Article
- Old cogs, new tricks: the evolution of gene expression in a chromatin context.Nature reviews. Genetics · 2019Review
- Specialized plant biochemistry drives gene clustering in fungi.The ISME journal · 2018Article
- Invisible cities: segregated domains in the yeast genome with distinct structural and functional attributes.Current genetics · 2018Article
- Structure and Chromosomal Organization of Yeast Genes Regulated by Topoisomerase II.International journal of molecular sciences · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The eukaryotic genome evolves under the dual constraint of maintaining coordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through the function of DNA topoisomerases, as has been shown in the concurrent transcriptional activation and suppression of genes upon transient deactivation of topoisomerase II (topoII). By analyzing a genome-wide transcription run-on experiment upon thermal inactivation of topoII in Saccharomyces cerevisiae we were able to define 116 gene clusters of consistent response (either positive or negative) to topological stress. A comprehensive analysis of these topologically co-regulated gene clusters reveals pronounced preferences regarding their functional, regulatory and structural attributes. Genes that negatively respond to topological stress, are positioned in gene-dense pericentromeric regions, are more conserved and associated to essential functions, while upregulated gene clusters are preferentially located in the gene-sparse nuclear periphery, associated with secondary functions and under complex regulatory control. We propose that genome architecture evolves with a core of essential genes occupying a compact genomic 'old town', whereas more recently acquired, condition-specific genes tend to be located in a more spacious 'suburban' genomic periphery.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.