Evidence map›Paper›PMID 23399596›Full record

ArticleCell research2013

Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming.

Shinpei Yamaguchi, Kwonho Hong, Rui Liu, Azusa Inoue, Li Shen, Kun Zhang, Yi Zhang

Abstract read
In one paragraph

Article in Cell research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.

0numbers the graph read from it
0cells of the map it votes in
103citing 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

103 citing papers in PubMed.

  1. Review
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  8. Review
  9. TET1 overexpression affects cell proliferation and apoptosis in aging ovaries.Journal of assisted reproduction and genetics · 2024
    Article
  10. DNMT1 can induce primary germ layer differentiation through de novo DNA methylation.Genes to cells : devoted to molecular & cellular mechanisms · 2024
    Article
  11. Article
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  14. Article
  15. Review
  16. Article
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  20. Article

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

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Shinpei YamaguchiHoward Hughes Medical Institute, WAB-149G, 200 Longwood Av., Boston, MA 02115, USA.
Kwonho Hong
Rui Liu
Azusa Inoue
Li Shen
Kun Zhang
Yi Zhang

Funding

Epigenetic and chemical approaches to generate function beta cellsU01DK089565 · NIDDK · UNIV OF NORTH CAROLINA CHAPEL HILL · PI ZHANG, YI · 2010 to 2014
$3.0M
Mechanisms of Polycomb SilencingR01GM068804 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI ZHANG, YI · 2003 to 2010
$2.1M
Genome-methylome InteractionsR01GM097253 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZHANG, KUN · 2011 to 2014
$1.4M
Howard Hughes Medical InstituteNIDDK NIH HHS U01 DK089565NIDDK NIH HHS U01DK089565NIGMS NIH HHS GM68804NIGMS NIH HHS R01 GM068804NIGMS NIH HHS R01 GM097253NIGMS NIH HHS R01GM097253
6 · The paper itself

Abstract

Previous studies have revealed that mouse primordial germ cells (PGCs) undergo genome-wide DNA methylation reprogramming to reset the epigenome for totipotency. However, the precise 5-methylcytosine (5mC) dynamics and its relationship with the generation of 5-hydroxymethylcytosine (5hmC) are not clear. Here we analyzed the dynamics of 5mC and 5hmC during PGC reprograming and germ cell development. Unexpectedly, we found a specific period (E8.5-9.5) during which both 5mC and 5hmC levels are low. Subsequently, 5hmC levels increase reaching its peak at E11.5 and gradually decrease until E13.5 likely by replication-dependent dilution. Interestingly, 5hmC is enriched in chromocenters during this period. While this germ cell-specific 5hmC subnuclear localization pattern is maintained in female germ cells even in mature oocytes, such pattern is gradually lost in male germ cells as mitotic proliferation resumes during the neonatal stage. Pericentric 5hmC plays an important role in silencing major satellite repeat, especially in female PGCs. Global transcriptome analysis by RNA-seq revealed that the great majority of differentially expressed genes from E9.5 to 13.5 are upregulated in both male and female PGCs. Although only female PGCs enter meiosis during the prenatal stage, meiosis-related and a subset of imprinted genes are significantly upregulated in both male and female PGCs at E13.5. Thus, our study not only reveals the dynamics of 5mC and 5hmC during PGC reprogramming and germ cell development, but also their potential role in epigenetic reprogramming and transcriptional regulation of meiotic and imprinted genes.

Indexed as

5-MethylcytosineAnimalsCytosineDNA MethylationEpigenesis, GeneticFemaleGene Expression Regulation, DevelopmentalGenomic ImprintingGerm CellsHeterochromatinMaleMice5-hydroxymethylcytosine5-MethylcytosineCytosineHeterochromatin

Identifiers

PMID23399596
PMCPMC3587712

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Registered trials

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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.