1. Developmental Biology
  2. Genetics and Genomics

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse

  1. Marco Morselli  Is a corresponding author
  2. William A Pastor
  3. Barbara Montanini
  4. Kevin Nee
  5. Roberto Ferrari
  6. Kai Fu
  7. Giancarlo Bonora
  8. Liudmilla Rubbi
  9. Amander T Clark
  10. Simone Ottonello
  11. Steven E Jacobsen
  12. Matteo Pellegrini
  1. University of California, Los Angeles, United States
  2. Laboratory of Functional Genomics and Protein Engineering, Italy
https://doi.org/10.7554/eLife.06205
Share this article
Cite this article
  1. Marco Morselli
  2. William A Pastor
  3. Barbara Montanini
  4. Kevin Nee
  5. Roberto Ferrari
  6. Kai Fu
  7. Giancarlo Bonora
  8. Liudmilla Rubbi
  9. Amander T Clark
  10. Simone Ottonello
  11. Steven E Jacobsen
  12. Matteo Pellegrini
(2015)
In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse
eLife 4:e06205.
https://doi.org/10.7554/eLife.06205
  2. Download BibTeX
  3. Download .RIS

Abstract

Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. Our data demonstrate that DNMT3B and H3K4 methylation are mutually exclusive and that DNMT3B is co-localized with H3K36 methylated regions. In support of this observation, DNA methylation analysis in yeast strains without Set1 and Set2 show an increase of relative 5meC levels at the TSS and a decrease in the gene-body, respectively. We extend our observation to the murine male germline, where H3K4me3 is strongly anti-correlated while H3K36me3 correlates with accelerated DNA methylation. These results show the importance of H3K36 methylation for gene-body DNA methylation in vivo.

Article and author information

Author details

  1. Marco Morselli

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    For correspondence
    mmorselli@ucla.edu
    Competing interests
    The authors declare that no competing interests exist.

  2. William A Pastor

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Barbara Montanini

    Biochemistry and Molecular Biology Unit, Department of Life Sciences, Laboratory of Functional Genomics and Protein Engineering, Parma, Italy
    Competing interests
    The authors declare that no competing interests exist.

  4. Kevin Nee

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Roberto Ferrari

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Kai Fu

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Giancarlo Bonora

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Liudmilla Rubbi

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Amander T Clark

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Simone Ottonello

    Biochemistry and Molecular Biology Unit, Department of Life Sciences, Laboratory of Functional Genomics and Protein Engineering, Parma, Italy
    Competing interests
    The authors declare that no competing interests exist.

  11. Steven E Jacobsen

    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  12. Matteo Pellegrini

    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

Ethics

Animal experimentation: All animal experimentation was conducted with the highest ethical standards in accordance with UCLA policy and procedures (DHHS OLAW A3196-01, AAALAC #000408 and protocol # 2008-070), and applicable provisions of the USDA Animal Welfare Act Regulations, the Public Health Service Policy on Humane Care and Use of Laboratory Animals, and the Guide for the Care and Use of Laboratory Animals.

Reviewing Editor

  1. Bing Ren, University of California, San Diego School of Medicine, United States

Publication history

  1. Received: December 20, 2014
  2. Accepted: April 2, 2015
  3. Accepted Manuscript published: April 7, 2015 (version 1)
  4. Accepted Manuscript updated: April 8, 2015 (version 2)
  5. Version of Record published: April 29, 2015 (version 3)
  6. Version of Record updated: August 31, 2017 (version 4)

Copyright

© 2015, Morselli 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

  • 7,097
    Page views
  • 1,402
    Downloads
  • 117
    Citations

Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, 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. Marco Morselli
  2. William A Pastor
  3. Barbara Montanini
  4. Kevin Nee
  5. Roberto Ferrari
  6. Kai Fu
  7. Giancarlo Bonora
  8. Liudmilla Rubbi
  9. Amander T Clark
  10. Simone Ottonello
  11. Steven E Jacobsen
  12. Matteo Pellegrini
(2015)
In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse
eLife 4:e06205.
https://doi.org/10.7554/eLife.06205

Categories and tags

Research organisms

Further reading

    1. Developmental Biology

    Npr3 regulates neural crest and cranial placode progenitors formation through its dual function as clearance and signaling receptor

    Arun Devotta, Hugo Juraver-Geslin ... Jean-Pierre Saint-Jeannet
    Research Article Updated

    Natriuretic peptide signaling has been implicated in a broad range of physiological processes, regulating blood volume and pressure, ventricular hypertrophy, fat metabolism, and long bone growth. Here, we describe a completely novel role for natriuretic peptide signaling in the control of neural crest (NC) and cranial placode (CP) progenitors formation. Among the components of this signaling pathway, we show that natriuretic peptide receptor 3 (Npr3) plays a pivotal role by differentially regulating two developmental programs through its dual function as clearance and signaling receptor. Using a combination of MO-based knockdowns, pharmacological inhibitors and rescue assays we demonstrate that Npr3 cooperate with guanylate cyclase natriuretic peptide receptor 1 (Npr1) and natriuretic peptides (Nppa/Nppc) to regulate NC and CP formation, pointing at a broad requirement of this signaling pathway in early embryogenesis. We propose that Npr3 acts as a clearance receptor to regulate local concentrations of natriuretic peptides for optimal cGMP production through Npr1 activation, and as a signaling receptor to control cAMP levels through inhibition of adenylyl cyclase. The intracellular modulation of these second messengers therefore participates in the segregation of NC and CP cell populations.

    1. Developmental Biology
    2. Evolutionary Biology

    Mutation of vsx genes in zebrafish highlights the robustness of the retinal specification network

    Joaquín Letelier, Lorena Buono ... Juan R Martínez-Morales
    Research Article

    Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors’ specification, and a later requirement for bipolar-cells fate determination. Despite their conserved expression patterns, it is currently unclear to which extent Vsx functions are also conserved across vertebrates, as mutant models are available only in mammals. To gain insight into vsx function in teleosts, we have generated vsx1 and vsx2 CRISPR/Cas9 double knockouts (vsxKO) in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae, with retinal precursors being rerouted toward photoreceptor or Müller glia fates. Surprisingly, neural retina is properly specified and maintained in mutant embryos, which do not display microphthalmia. We show that although important cis-regulatory remodelling occurs in vsxKO retinas during early specification, this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network, and to Vsx genes regulatory weight varying substantially among vertebrate species.