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Connectron Dynamics

This document introduces Connectron Dynamics, a conceptual framework designed to illustrate how simple Connectron patterns can contribute to complex transcription behaviors in genes and non-coding RNAs. It elucidates the rules governing transcription regulation and presents visual representations of these dynamics. Through simulations, the resulting "music" reflects the transcription processes influenced by Connectrons. The exploration includes manipulating lifetimes and connectivity of one-shot Connectrons, leading to varied transcription behaviors and unique interactions within the eukaryotic transcriptome, with applications in understanding genome dynamics.

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Connectron Dynamics

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  1. Connectron Dynamics Richard J. Feldmann Global Determinants, Inc. Derwood, Maryland 20855, USA rjfeldma@globaldeterminants.com

  2. The goals of the Connectron Dynamics Examples • To show how simple Connectron patterns can build up complex gene and non-coding RNA transcription behaviors • To develop a conceptual framework for analyzing the behavior of large eukaryotic transcriptomes.

  3. How the Connectron Dynamics Examples work • Rules determine which gene or non-coding RNA causes the repression of transcription of which other genes or non-coding RNAs. • The graphic present the rules in a visual form. • The “music score” is the result of the simulation of the behavior of the rules. • The sound is the “music” of the simulation.

  4. The transcription of a single gene or non-coding RNA is controlled only the transcription factors

  5. The transcription of two genes or non-coding RNAs is controlled independently by their transcription factors

  6. A genes or non-coding RNA that generates a Connectron turns off the transcription of another gene or non-coding RNA

  7. A gene or non-coding RNA can use a Connectron to turn off its own transcription.

  8. A “one-shot” connectron can turn off the transcription of another gene or non-coding RNA.

  9. Two one-shot Connectrons transcribe independently.

  10. One one-shot Connectron can drive another one-shot Connectron

  11. Changing the lifetime of the second one-shot Connectron changes the “music” of the behavior

  12. A short lifetime of the second one-shot locks its behavior to the driving one-shot.

  13. Playing with the lifetimes produces different behaviors.

  14. A third one-shot runs independently

  15. Coupling the one-shots produces a particular behavior.

  16. Playing with the connectivity produces different behaviors.

  17. This coupling produces an interesting behavior.

  18. Playing with the lifetimes produces another behavior.

  19. The two sets of one-shot Connectrons are running independently.

  20. Two sets of three one-shots coupled together produces an interesting behavior.

  21. This coupled behavior is quite different.

  22. Two sets of six one-shots running independently.

  23. The four sets of Connectrons are coupled thus producing a very interesting behavior.

  24. The Connectrome of a “Toy” Genome

  25. The Connectrome of the Transcriptome of the Mouse Genome

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