Evidence map›Paper›PMID 31955845›Full record

ArticleCell2020

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase.

Sandra Catania, Phillip A Dumesic, Harold Pimentel, Ammar Nasif, Caitlin I Stoddard, Jordan E Burke, Jolene K Diedrich, Sophie Cook, Terrance Shea, Elizabeth Geinger and 7 more

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 62 papers.

0numbers the graph read from it
0cells of the map it votes in
62citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

62 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Review
  5. Article
  6. Article
  7. Review
  8. Article
  9. Article
  10. Review
  11. Article
  12. Article
  13. New perspectives on DNA methylation modifications in ocular diseases.International journal of ophthalmology · 2025
    Review
  14. Transposon load and RNAi loss synergize to drive intraspecies diversity inProceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Review
  20. Thyroid hormone links environmental signals to DNA methylation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024
    Review

2 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors.

Sandra CataniaDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Phillip A DumesicDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Harold PimentelHoward Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Ammar NasifMRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK.
Caitlin I StoddardDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Jordan E BurkeDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Jolene K DiedrichDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
Sophie CookDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Terrance SheaInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Elizabeth GeingerInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Robert LintnerInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
John R YatesDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
Petra HajkovaMRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK.
Geeta J NarlikarDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Christina A CuomoInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Jonathan K PritchardDepartment of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Hiten D MadhaniDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address: hitenmadhani@gmail.com.

Funding

MEDICAL SCIENTIST TRAINING PROGRAMT32GM007618 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANDERSON, MARK S · 1985 to 2020
$29.6M
TrainingP41GM103533 · NIGMS · UNIVERSITY OF WASHINGTON · PI MACCOSS, MICHAEL · 2012 to 2021
$20.7M
Rapid production of SARS-CoV-2 molecular clones using CRISPR-based yeast recombineeringR01AI100272 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MADHANI, HITEN D · 2012 to 2025
$11.3M
Mechanisms of Gene SilencingR01GM071801 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Hiten D Madhani · 2005 to 2026
$7.1M
Epigenetic control of virulence in a fungal meningitis pathogenR01AI120464 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MADHANI, HITEN D · 2015 to 2019
$1.9M
Medical Research Council MC_U120092689Medical Research Council MC_US_A652_5PY70NIAID NIH HHS R01 AI100272NIAID NIH HHS R01 AI120464NIGMS NIH HHS P41 GM103533NIGMS NIH HHS R01 GM071801NIGMS NIH HHS T32 GM007618
6 · The paper itself

Abstract

Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 mya. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 million years through a process analogous to Darwinian evolution of the genome.

Indexed as

Biological EvolutionCryptococcus neoformansDNADNA (Cytosine-5-)-Methyltransferase 1DNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Modification MethylasesDNA Transposable ElementsEpigenomicsEvolution, MolecularGenomeMethyltransferasesPhylogenyDNADNA (Cytosine-5-)-Methyltransferase 1DNA (Cytosine-5-)-MethyltransferasesDNA Modification MethylasesDNA Transposable ElementsMethyltransferaseschromatinCryptocococcus neoformansDNA methylationepigenetic memoryepigeneticsevolutiontransposable elements

Identifiers

PMID31955845
PMCPMC7197499

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.