Gene regulatory network stabilized by pervasive weak repressions: microRNA functions revealed by the May–Wigner theory

Chen, Yuxin; Shen, Yang; Lin, Pei; Ding, Tao; Zhao, Yixin; Allesina, Stefano; Shen, Xu; Wu, Chung‐I

doi:10.1093/nsr/nwz076

Cited by 39 publications

(57 citation statements)

References 76 publications

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“…S2 , Supplementary Material online), which might be relevant to the general role miRNAs playing in stabilizing gene regulatory network ( Zhao et al. 2017 , 2018 ; Ambros 2019; Chen et al. 2019 ).…”

Section: Resultsmentioning

confidence: 99%

Run or Die in the Evolution of New MicroRNAs—Testing the Red Queen Hypothesis on De Novo New Genes

Zhao

Yang

et al. 2020

Molecular Biology and Evolution

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The Red Queen hypothesis depicts evolution as the continual struggle to adapt. According to this hypothesis, new genes, especially those originating from nongenic sequences (i.e., de novo genes), are eliminated unless they evolve continually in adaptation to a changing environment. Here, we analyze two Drosophila de novo miRNAs that are expressed in a testis-specific manner with very high rates of evolution in their DNA sequence. We knocked out these miRNAs in two sibling species and investigated their contributions to different fitness components. We observed that the fitness contributions of miR-975 in Drosophila simulans seem positive, in contrast to its neutral contributions in D. melanogaster, whereas miR-983 appears to have negative contributions in both species, as the fitness of the knockout mutant increases. As predicted by the Red Queen hypothesis, the fitness difference of these de novo miRNAs indicates their different fates.

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Section: Resultsmentioning

confidence: 99%

Run or Die in the Evolution of New MicroRNAs—Testing the Red Queen Hypothesis on De Novo New Genes

Zhao

Yang

et al. 2020

Molecular Biology and Evolution

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“…Based on RMT, one may expect faster degradation to stabilize the system. This has in fact been argued to be the case 5,6 . However, by taking into account the dynamics of protein concentrations and how it couples to the dynamics of mRNA levels, we find that this is not the case.…”

Section: Discussionmentioning

confidence: 96%

“…This approach has also been used to analyze other large interacting systems. In particular, it has been used to argue why weak repressions by microRNAs, thought of as effectively increasing the degradation rate of mRNAs, confer stability to gene regulatory networks 5 , 6 . However, such a framework does not take into account the functional form of f i and in particular that the matrix elements often depend on the steady-state solutions themselves.…”

Section: Introductionmentioning

confidence: 99%

Exploring the effect of network topology, mRNA and protein dynamics on gene regulatory network stability

Guo

Amir

2021

Nat Commun

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Homeostasis of protein concentrations in cells is crucial for their proper functioning, requiring steady-state concentrations to be stable to fluctuations. Since gene expression is regulated by proteins such as transcription factors (TFs), the full set of proteins within the cell constitutes a large system of interacting components, which can become unstable. We explore factors affecting stability by coupling the dynamics of mRNAs and proteins in a growing cell. We find that mRNA degradation rate does not affect stability, contrary to previous claims. However, global structural features of the network can dramatically enhance stability. Importantly, a network resembling a bipartite graph with a lower fraction of interactions that target TFs has a higher chance of being stable. Scrambling the E. coli transcription network, we find that the biological network is significantly more stable than its randomized counterpart, suggesting that stability constraints may have shaped network structure during the course of evolution.

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“…Leaves from each individual were dried, labeled, and stored for DNA extraction. DNA was extracted using the modified CTAB method (Doyle & Doyle, 1987). DNA content of each extraction was measured by NanoDrop 2000.…”

Section: Morphological Characters Sampling and Dna Extractionmentioning

confidence: 99%

Genomic landscape of subspecies defined by phenotypic criteria：Analyses of the mangrove species complex, Avicennia marina

Wang¹,

Guo²,

Zhong

et al. 2020

Preprint

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Subspecies designation is widely used to describe taxa below species but above geographical populations. What patterns of genomic variation is expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina of the Indo-West Pacific coasts. This species has three subspecies, distinguished by morphological traits and geographical distribution. We collected samples from 16 populations (577 individuals) covering all three subspecies and sequenced 94 nuclear genes. We reveal comprehensive genetic divergence among subspecies, generally higher than among geographical populations within subspecies. The level of genetic diversity differs among the three subspecies, possibly hinting at a degree of separation among their gene pools. We observed that divergence varies from locus to locus across the genome. A small portion of the genome is most informative about subspecies delineation while the rest is undifferentiated or slightly differentiated, hinting at uneven gene flow and incomplete isolation. The three subspecies likely split simultaneously with gene flow among lineages. This reticulate evolution results in some discordance between morphology and genetics in areas of population contact. In short, A. marina subspecies show species-like patterns in some respects and population-like patterns in others. This "ambiguity" is expected at a stage between structured populations and full species, thus the observed patterns strengthen the subspecies designation. We propose that subspecies designation is informative in predicting genomic landscape of divergences and useful in making conservation decisions.

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Gene regulatory network stabilized by pervasive weak repressions: microRNA functions revealed by the May–Wigner theory

Cited by 39 publications

References 76 publications

Run or Die in the Evolution of New MicroRNAs—Testing the Red Queen Hypothesis on De Novo New Genes

Run or Die in the Evolution of New MicroRNAs—Testing the Red Queen Hypothesis on De Novo New Genes

Exploring the effect of network topology, mRNA and protein dynamics on gene regulatory network stability

Genomic landscape of subspecies defined by phenotypic criteria：Analyses of the mangrove species complex, Avicennia marina

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