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Journal Articles Nature Reviews Genetics Year : 2020

Redefining fundamental concepts of transcription initiation in bacteria

Citlalli Mejía-Almonte
  • Function : Author
Stephen Busby
  • Function : Author
Joseph Wade
  • Function : Author
Adam Arkin
  • Function : Author
Gary Stormo
  • Function : Author
Karen Eilbeck
  • Function : Author
Bernhard Palsson
  • Function : Author
James Galagan
Julio Collado-Vides
  • Function : Author


Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.

Dates and versions

hal-03139472 , version 1 (12-02-2021)



Citlalli Mejía-Almonte, Stephen Busby, Joseph Wade, Jacques van Helden, Adam Arkin, et al.. Redefining fundamental concepts of transcription initiation in bacteria. Nature Reviews Genetics, 2020, 21 (11), pp.699-714. ⟨10.1038/s41576-020-0254-8⟩. ⟨hal-03139472⟩


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