Menu

Close

Genetic compensation is triggered by mutant mRNA degradation

Mohamed El-Brolosy, Andrea Rossi, Zacharias Kontarakis, Carsten Kuenne, Stefan Guenther, Nana Fukuda, Carter Takacs, Shih-Lei Lai, Ryuichi Fukuda, Claudia Gerri, Khrievono Kikhi, Antonio Giraldez, Didier Y.R. Stainier

Preprint posted on May 22, 2018 https://www.biorxiv.org/content/early/2018/05/22/328153

Nonsense mediated decay of mutant mRNA can trigger genetic compensation via specific transcriptional upregulation of related genes in stable knock-out models.

Selected by Andreas van Impel

Background

In the last years, advances in TALEN and CRISPR genome editing technologies have made it reasonably easy to generate loss of function alleles for any given gene in many model systems used. These reverse genetic approaches led to a number of reports describing evident discrepancies between stable genetic knock-out models and results obtained by knock-down strategies (e.g. morpholino antisense oligomers or siRNAs) for the same gene. In most cases these phenotypic differences have been attributed to off-target hits or toxic effects of the employed knock-down reagents [1]. One study in zebrafish, however, reported on the upregulation of related genes in mutants but not after using transcriptional or translational knock-down approaches, suggesting that the phenotypic differences can be explained by a specific compensatory response in the knock-out but not the knock-down models for this gene [2]. Whether such a genetic compensation represents a general phenomenon that applies to many mutant situations and that -to some extent- protects organisms against deleterious mutations remains unclear. Furthermore it is not known how such transcriptional adaption responses are triggered in the mutant situation and how this could be possibly circumvented when generating novel mutant alleles.

 

Key findings

The authors of this preprint tackle the question at which level and via which signal a genetic compensation mechanism can trigger the upregulation of related genes that partially or even fully compensate for the loss of the respective gene function. Using zebrafish and mouse models, the authors report for a number of mutants a transcriptional upregulation of paralogues or related family members of the mutant gene, even in the heterozygous state. Injection of the respective wild type mRNA does not reduce this response, indicating that the compensation mechanism is activated upstream of the loss of functional protein. They further show that for several of the genes analysed other nonsense mutation alleles exist that do not show transcriptional adaptation arguing against the DNA lesion itself to activate the response. However, when checking the amount of mutant mRNA present in those alleles, El-Brolosy et al. observe a strong correlation between the extent of the transcriptional adaptation response and the levels of mutant mRNA decay. In line with this finding, blockage of the nonsense mediated decay pathway results in higher mutant mRNA levels and consequently in a reduced or absent transcriptional adaptation response. Even injection of uncapped (and therefore instable) mRNA is sufficient to trigger transcriptional adaptation in a sequence-similarity specific manner, suggesting that degradation-intermediates of the mRNA decay pathway might initiate the compensatory response (see figure).

Finally the authors generate CRISPR-induced promoter (or whole gene) deletions to obtain alleles in which the mutant mRNA is not even transcribed in the first place. Importantly, these ‘RNA-less’ mutants fail to upregulate compensating genes, suggesting that the generation of such alleles could circumvent the here described genetic compensation mechanisms and unravel phenotypes that would have normally been masked by transcriptional adaptation.

 

Model showing the proposed mechanism underlying the transcriptional adaption response to mutations. Red dot: mutation, PTC: premature termination codon, TC: termination codon, DFs: degradation factors, RBPs: RNA binding proteins (reproduced from El-Brolosy et al., Fig. 4 )

 

Why this is important

The work from El-Brolosy et al. indicates the existence of a conserved mechanism triggering genetic compensation via transcriptional upregulation of related genes. This compensation seems to be based on the instability of the mutant mRNA and the related availability of mRNA degradation products in the cells. Although the exact molecular mechanism of this response still remains enigmatic, the presented work clearly argues for the generation and analysis of knock-out models, in which the transcription of the gene is blocked completely (e.g. via deletion of the whole promoter region). Such an approach should minimize the risk of transcriptional adaptation-derived compensation effects masking a possible requirement for the gene of interest. Hence, producing ‘RNA-less’ alleles represents an important strategy for the CRISPR- and TALEN-mediated generation of novel mutants in different model systems in the future.

 

Open questions

  • How exactly is the presence of mRNA degradation products transduced into a specific transcriptional upregulation of related genes? What molecular machinery is involved in this process?
  • How frequent is this type of mRNA decay-dependent genetic compensation? Is it a general phenomenon that is applicable for most/many genes in the genome?
  • Is this pathway conserved throughout evolution (e.g. in Arabidopsis, yeast and Drosophila)?

 

Further reading

[1]          Kok, F. O. et al. Reverse Genetic Screening Reveals Poor Correlation between Morpholino-Induced and Mutant Phenotypes in Zebrafish. Dev Cell. 32:97±108 (2015).

[2]          Rossi, A. et al. Genetic compensation induced by deleterious mutations but not gene knockdowns. Nature 524, 230-233 (2015).

[3]          El-Brolosy, M. A. & Stainier, D. Y. R. Genetic compensation: A phenomenon in search of mechanisms. PLoS genetics 13 (2017).

Tags: genetic robustness, genome engineering

Posted on: 5th June 2018 , updated on: 19th June 2018

Read preprint (No Ratings Yet)




  • Author's response

    Mohamed El-Brolosy and Didier Stainier shared

    How exactly is the presence of mRNA degradation products transduced into a specific transcriptional upregulation of related genes? What molecular machinery is involved in this process?

    Previous studies have reported that mRNA decay factors can translocate to the nucleus (in a manner dependent on their ability to degrade mRNA) and bind chromatin to promote gene expression (for example: Haimovich et al., Cell 2013).  Other studies have reported genetic and physical interactions of several decay factors with a number of proteins involved in gene expression including RNA pol II, chromatin remodelers and histone modifying enzymes.  As we show in Fig. 4a, a majority of the genes exhibiting sequence similarity with the mutated gene’s mRNA are upregulated in the mutant cells, suggesting a model whereby mRNA decay products guide mRNA decay factors to specific genes in a homology-mediated base-pairing fashion.  Other models are of course also possible, and the transcriptional adaptation response might in addition involve antisense or non-coding RNAs (Fig. S10).

     

    How frequent is this type of mRNA decay-dependent genetic compensation? Is it a general phenomenon that is applicable for most/many genes in the genome?

    The transcriptional adaptation machinery via mRNA decay appears to be using broadly expressed components; however, it is important to note that this transcriptional adaptation response will not always lead to functional compensation as the upregulated genes may not be able to assume the function of the mutated gene.

     

    Is this pathway conserved throughout evolution (e.g. in Arabidopsis, yeast and Drosophila)?

    Genetic compensation is observed in many organisms (El-Brolosy and Stainier, PLOS Genetics 2017). For example, a lack of phenotypes was reported for several Arabidopsis mutants (Bouche and Bouchez, Curr. Opinion in Plant Biology2001); in C. elegans, incomplete penetrance of skn1 mutants was attributed to variability in expression levels of the compensating gene end-1 (Raj et al., Nature 2010);and in Drosophila, there are several examples of discrepancy between knockout and knockdown phenotypes, which might be due to genetic compensation (Yamamoto et al., Cell 2014).  Of course, one has to investigate each individual case in detail and determine whether transcriptional adaptation and mRNA decay are involved; we are currently conducting studies in yeast and C. elegans.

    Have your say

    Your email address will not be published. Required fields are marked *

    Sign up to customise the site to your preferences and to receive alerts

    Register here

    Also in the developmental biology category:

    Revealing the nanoscale morphology of the primary cilium using super-resolution fluorescence microscopy

    Joshua Yoon, Colin J. Comerci, Lucien E. Weiss, et al.



    Selected by Gautam Dey

    Signaling dynamics control cell fate in the early Drosophila embryo

    Heath E Johnson, Stanislav Y Shvartsman, Jared E Toettcher



    Selected by Yara E. Sánchez Corrales

    1

    Three-dimensional tissue stiffness mapping in the mouse embryo supports durotaxis during early limb bud morphogenesis

    Min Zhu, Hirotaka Tao, Mohammad Samani, et al.



    Selected by Natalie Dye

    PUMILIO hyperactivity drives premature aging of Norad-deficient mice

    Florian Kopp, Mehmet Yalvac, Beibei Chen, et al.



    Selected by Carmen Adriaens

    Synergy with TGFβ ligands switches WNT pathway dynamics from transient to sustained during human pluripotent cell differentiation

    Joseph Massey, Yida Liu, Omar Alvarenga, et al.



    Selected by Pierre Osteil

    1

    3D Tissue elongation via ECM stiffness-cued junctional remodeling

    Dong-Yuan Chen, Justin Crest, Sebastian J Streichan, et al.



    Selected by Sundar Naganathan

    EGFR signaling coordinates patterning with cell survival during Drosophila epidermal development

    Samuel Henry Crossman, Sebastian J Streichan, Jean-Paul Vincent



    Selected by Sarah Bowling

    1

    Damage-induced reactive oxygen species enable zebrafish tail regeneration by repositioning of Hedgehog expressing cells.

    Henry Roehl, Montserrat Garcia Romero, Gareth McCathie, et al.



    Selected by Alberto Rosello-Diez

    Arterio-Venous Remodeling in the Zebrafish Trunk Is Controlled by Genetic Programming and Flow-Mediated Fine-Tuning

    Ilse Geudens, Baptiste Coxam, Silvanus Alt, et al.



    Selected by Andreas van Impel

    Developmental heterogeneity of microglia and brain myeloid cells revealed by deep single-cell RNA sequencing

    Qingyun Li, Zuolin Cheng, Lu Zhou, et al.



    Selected by Zheng-Shan Chong

    Polyacrylamide Bead Sensors for in vivo Quantification of Cell-Scale Stress in Zebrafish Development

    Nicole Traeber, Klemens Uhlmann, Salvatore Girardo, et al.



    Selected by Jacky G. Goetz

    millepattes micropeptides are an ancient developmental switch required for embryonic patterning

    Suparna Ray, Miriam I Rosenberg, Hélène Chanut-Delalande, et al.



    Selected by Erik Clark

    Aurora A depletion reveals centrosome-independent polarization mechanism in C. elegans

    Kerstin Klinkert, Nicolas Levernier, Peter Gross, et al.

    AND

    Centrosome Aurora A gradient ensures a single PAR-2 polarity axis by regulating RhoGEF ECT-2 localization in C. elegans embryos

    Sachin Kotak, Sukriti Kapoor



    Selected by Giuliana Clemente

    Anti-angiogenic effects of VEGF stimulation on endothelium deficient in phosphoinositide recycling

    Amber N Stratman, Olivia M Farrelly, Constantinos M Mikelis, et al.



    Selected by Coert Margadant

    SOL1 and SOL2 Regulate Fate Transition and Cell Divisions in the Arabidopsis Stomatal Lineage

    Abigail R Simmons, Kelli A Davies, Wanpeng Wang, et al.



    Selected by Martin Balcerowicz

    Analysis of the role of Nidogen/entactin in basement membrane assembly and morphogenesis in Drosophila

    Jianli Dai, Beatriz Estrada, Sofie Jacobs, et al.



    Selected by Nargess Khalilgharibi

    Also in the genetics category:

    Signaling dynamics control cell fate in the early Drosophila embryo

    Heath E Johnson, Stanislav Y Shvartsman, Jared E Toettcher



    Selected by Yara E. Sánchez Corrales

    1

    PUMILIO hyperactivity drives premature aging of Norad-deficient mice

    Florian Kopp, Mehmet Yalvac, Beibei Chen, et al.



    Selected by Carmen Adriaens

    Arterio-Venous Remodeling in the Zebrafish Trunk Is Controlled by Genetic Programming and Flow-Mediated Fine-Tuning

    Ilse Geudens, Baptiste Coxam, Silvanus Alt, et al.



    Selected by Andreas van Impel

    CRISPR/Cas9-mediated gene deletion of the ompA gene in an Enterobacter gut symbiont impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes

    Shivanand Hegde, Pornjarim Nilyanimit, Elena Kozlova, et al.



    Selected by Snehal Kadam

    millepattes micropeptides are an ancient developmental switch required for embryonic patterning

    Suparna Ray, Miriam I Rosenberg, Hélène Chanut-Delalande, et al.



    Selected by Erik Clark

    Neural crest cells regulate optic cup morphogenesis by promoting extracellular matrix assembly

    Chase Dallas Bryan, Rebecca Lynne Pfeiffer, Bryan William Jones, et al.



    Selected by Ashrifia Adomako-Ankomah

    1

    The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila



    Selected by Clarice Hong

    1

    Dynamic control of proinflammatory cytokines Il-1β and Tnf-α by macrophages is necessary for functional spinal cord regeneration in zebrafish

    Themistoklis M. Tsarouchas, Daniel Wehner, Leonardo Cavone, et al.



    Selected by Shikha Nayar

    1

    JNK-mediated spindle reorientation in stem cells promotes dysplasia in the aging intestine

    Daniel Hu, Heinrich Jasper



    Selected by Maiko Kitaoka

    Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions

    Summer B. Thyme, Lindsey M. Pieper, Eric H. Li, et al.



    Selected by Daniel Grimes

    Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline

    Hannah A. Grunwald, Valentino M. Gantz, Gunnar Poplawski, et al.



    Selected by Rebekah Tillotson

    1

    The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization

    Sarah Herberg, Krista R Gert, Alexander Schleiffer, et al.



    Selected by James Gagnon

    Functional testing of a human PBX3 variant in zebrafish reveals a potential modifier role in congenital heart defects

    Gist H. Farr III, Kimia Imani, Darren Pouv, et al.



    Selected by Hannah Brunsdon

    A robust method for transfection in choanoflagellates illuminates their cell biology and the ancestry of animal septins

    David Booth, Heather Middleton, Nicole King



    Selected by Maya Emmons-Bell

    SWI/SNF remains localized to chromatin in the presence of SCHLAP1

    Jesse R Raab, Keriayn N Smith, Camarie C Spear, et al.



    Selected by Carmen Adriaens

    1

    Genetic compensation is triggered by mutant mRNA degradation

    Mohamed El-Brolosy, Andrea Rossi, Zacharias Kontarakis, et al.



    Selected by Andreas van Impel

    1

    Close