Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise

Kun Xiong, Alex K. Lancaster, Mark Siegal, Joanna Masel

Research output: Contribution to journalArticle

Abstract

In transcriptional regulatory networks (TRNs), a canonical 3-node feed-forward loop (FFL) is hypothesized to evolve to filter out short spurious signals. We test this adaptive hypothesis against a novel null evolutionary model. Our mutational model captures the intrinsically high prevalence of weak affinity transcription factor binding sites. We also capture stochasticity and delays in gene expression that distort external signals and intrinsically generate noise. Functional FFLs evolve readily under selection for the hypothesized function but not in negative controls. Interestingly, a 4-node “diamond” motif also emerges as a short spurious signal filter. The diamond uses expression dynamics rather than path length to provide fast and slow pathways. When there is no idealized external spurious signal to filter out, but only internally generated noise, only the diamond and not the FFL evolves. While our results support the adaptive hypothesis, we also show that non-adaptive factors, including the intrinsic expression dynamics, matter.

Original languageEnglish (US)
Article number2418
JournalNature communications
Volume10
Issue number1
DOIs
StatePublished - Dec 1 2019

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Diamond
Noise
topology
Topology
diamonds
filters
Intrinsic Factor
Gene Regulatory Networks
Gene expression
gene expression
Transcription Factors
Binding Sites
affinity
Gene Expression

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise. / Xiong, Kun; Lancaster, Alex K.; Siegal, Mark; Masel, Joanna.

In: Nature communications, Vol. 10, No. 1, 2418, 01.12.2019.

Research output: Contribution to journalArticle

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