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Gene syntax defines supercoiling-mediated transcriptional feedback.

Christopher P Johnstone1, Kasey S Love2, Sneha R Kabaria1

  • 1Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA.

Biorxiv : the Preprint Server for Biology
|January 27, 2025
PubMed
Summary

Gene arrangement (syntax) influences gene expression through supercoiling-mediated feedback. This discovery enables the design of more efficient synthetic gene circuits by controlling gene order.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Systems Biology

Background:

  • Gene syntax, the arrangement of genes and regulatory elements, is crucial for coordinating gene circuits.
  • The molecular mechanisms underlying how gene order affects transcription of nearby genes are not well understood.

Purpose of the Study:

  • To investigate the role of gene syntax in regulating gene expression through supercoiling-mediated feedback.
  • To explore the application of syntax-based design in creating novel synthetic gene circuits.

Main Methods:

  • Utilized integrated reporter circuits in human cells to study gene expression.
  • Employed Region Capture Micro-C to analyze supercoiled plectoneme formation and syntax-specific chromatin structures.
  • Developed and tested compact synthetic gene circuits using gene syntax as a design parameter.

Main Results:

  • Demonstrated that supercoiling-mediated feedback regulates adjacent gene expression in a manner dependent on gene syntax.
  • Observed induction-dependent formation of supercoiled plectonemes and specific chromatin structures.
  • Successfully designed compact gene circuits with tunable expression characteristics (mean, variance, stoichiometry).

Conclusions:

  • Gene syntax is a critical factor in supercoiling-mediated gene regulation.
  • Understanding and manipulating gene syntax can enhance the design and efficiency of synthetic gene circuits.
  • Integrating supercoiling feedback into gene regulation models will improve both native system comprehension and synthetic biology applications.