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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Tsochatzidou M,Malliarou M,Papanikolaou N,Roca J,Nikolaou Cdoi
10.1093/nar/gkx198subject
Has Abstractpub_date
2017-06-02 00:00:00pages
5818-5828issue
10eissn
0305-1048issn
1362-4962pii
3079510journal_volume
45pub_type
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