The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis

  1. Sarah N Deffit
  2. Brian A Yee
  3. Aidan C Manning
  4. Suba Rajendren
  5. Pranathi Vadlamani
  6. Emily C Wheeler
  7. Alain Domissy
  8. Michael C Washburn
  9. Gene W Yeo  Is a corresponding author
  10. Heather A Hundley  Is a corresponding author
  1. Indiana University, United States
  2. University of California at San Diego, United States
  3. University of California, San Diego, United States

Abstract

ADAR proteins alter gene expression both by catalyzing adenosine (A) to inosine (I) RNA editing and binding to regulatory elements in target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. Caenorhabditis elegans lacking ADARs exhibit reduced chemotaxis, but the targets responsible for this phenotype remain unknown. To identify critical neural ADAR targets in C. elegans, we performed an unbiased assessment of the effects of ADR-2, the only A-to-I editing enzyme in C. elegans, on the neural transcriptome. Development and implementation of publicly available software, SAILOR, identified 7,361 A-to-I editing events across the neural transcriptome. Intersecting the neural editome with adr-2 associated gene expression changes, revealed an edited mRNA, clec-41, whose neural expression is dependent on deamination. Restoring clec-41 expression in adr-2 deficient neural cells rescued the chemotaxis defect, providing the first evidence that neuronal phenotypes of ADAR mutants can be caused by altered gene expression.

Article and author information

Author details

  1. Sarah N Deffit

    Medical Sciences Program, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Brian A Yee

    Department of Cellular and Molecular Medicine, Stem Cell Program, Institute for Genomic Medicine, University of California at San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Aidan C Manning

    Medical Sciences Program, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Suba Rajendren

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Pranathi Vadlamani

    Medical Sciences Program, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Emily C Wheeler

    Department of Cellular and Molecular Medicine, Stem Cell Program, Institute for Genomic Medicine, University of California at San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Alain Domissy

    Department of Cellular and Molecular Medicine, Stem Cell Program, Institute for Genomic Medicine, University of California at San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Michael C Washburn

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Gene W Yeo

    Department of Cellular and Molecular Medicine, Stem Cell Program, Institute for Genomic Medicine, University of California, San Diego, La Jolla, United States
    For correspondence
    geneyeo@ucsd.edu
    Competing interests
    The authors declare that no competing interests exist.
  10. Heather A Hundley

    Medical Sciences Program, Indiana University, Bloomington, United States
    For correspondence
    hahundle@indiana.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9106-9016

Funding

American Cancer Society (RSG-15-051-RMC)

  • Heather A Hundley

Indiana Clinical and Translational Sciences Institute

  • Sarah N Deffit

National Science Foundation

  • Emily C Wheeler

National Institutes of Health (1F32GM119257-01A1)

  • Sarah N Deffit

National Institutes of Health (T32GM00866)

  • Emily C Wheeler

National Institutes of Health (HG004659)

  • Gene W Yeo

National Institutes of Health (NS075449)

  • Gene W Yeo

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Oliver Hobert, Howard Hughes Medical Institute, Columbia University, United States

Publication history

  1. Received: May 14, 2017
  2. Accepted: September 18, 2017
  3. Accepted Manuscript published: September 19, 2017 (version 1)
  4. Version of Record published: October 17, 2017 (version 2)
  5. Version of Record updated: October 23, 2017 (version 3)
  6. Version of Record updated: February 12, 2018 (version 4)

Copyright

© 2017, Deffit et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,528
    Page views
  • 373
    Downloads
  • 19
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Sarah N Deffit
  2. Brian A Yee
  3. Aidan C Manning
  4. Suba Rajendren
  5. Pranathi Vadlamani
  6. Emily C Wheeler
  7. Alain Domissy
  8. Michael C Washburn
  9. Gene W Yeo
  10. Heather A Hundley
(2017)
The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
eLife 6:e28625.
https://doi.org/10.7554/eLife.28625

Further reading

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
    Feng He et al.
    Research Article

    A single Dcp1-Dcp2 decapping enzyme targets diverse classes of yeast mRNAs for decapping-dependent 5' to 3' decay, but the molecular mechanisms controlling mRNA selectivity by the enzyme remain elusive. Through extensive genetic analyses we reveal that Dcp2 C-terminal domain cis-regulatory elements control decapping enzyme target specificity by orchestrating formation of distinct decapping complexes. Two Upf1-binding motifs direct the decapping enzyme to NMD substrates, a single Edc3-binding motif targets both Edc3 and Dhh1 substrates, and Pat1-binding leucine-rich motifs target Edc3 and Dhh1 substrates under selective conditions. Although it functions as a unique targeting component of specific complexes, Edc3 is a common component of multiple complexes. Scd6 and Xrn1 also have specific binding sites on Dcp2, allowing them to be directly recruited to decapping complexes. Collectively, our results demonstrate that Upf1, Edc3, Scd6, and Pat1 function as regulatory subunits of the holo-decapping enzyme, controlling both its substrate specificity and enzymatic activation.

    1. Chromosomes and Gene Expression
    Faith C Fowler et al.
    Research Article Updated

    DNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs are predominately repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 murine and human cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in proliferating cells at the G1 or G2 phase of the cell cycle was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, which has important implications for DNA DSB repair in quiescent cells.