Evidence map›Paper›PMID 25071199›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2014

Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation.

Ageliki Tsagaratou, Tarmo Äijö, Chan-Wang J Lio, Xiaojing Yue, Yun Huang, Steven E Jacobsen, Harri Lähdesmäki, Anjana Rao

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.

0numbers the graph read from it
0cells of the map it votes in
122citing 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

122 citing papers in PubMed.

  1. Review
  2. TET1 deficiency amplifies macrophage inflammatory signaling associated with Crohn's disease.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026
    Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Cell identity and 5-hydroxymethylcytosine.Epigenetics & chromatin · 2025
    Review
  8. Article
  9. Article
  10. Review
  11. Article
  12. Article
  13. Review
  14. Article
  15. Review
  16. Article
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  18. Review
  19. Article
  20. Article

62 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

8 authors.

Ageliki TsagaratouDepartment of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92034;
Tarmo ÄijöDepartment of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92034;Department of Information and Computer Science, Aalto University School of Science, FI-00076 Aalto, Finland;
Chan-Wang J LioDepartment of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92034;
Xiaojing YueDepartment of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92034;
Yun HuangDepartment of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92034;Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037;
Steven E JacobsenHoward Hughes Medical Institute,Department of Molecular, Cell, and Developmental Biology, andEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095; and.
Harri LähdesmäkiDepartment of Information and Computer Science, Aalto University School of Science, FI-00076 Aalto, Finland;
Anjana RaoDepartment of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92034;Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037;Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093 arao@liai.org.

Funding

Epigenomics of T cells and innate immune cells in human asthmaR01HL114093 · NHLBI · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI ARSHAD, SYED HASAN, PETERS, BJOERN · 2011 to 2020
$8.5M
REGULATED ACCESSIBILITY OF A CYTOKINE GENE LOCUSR01AI044432 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI RAO, ANJANA · 1999 to 2014
$7.7M
Role of TET proteins in myeloid malignanciesR01CA151535 · NCI · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI RAO, ANJANA · 2012 to 2016
$1.8M
Howard Hughes Medical InstituteNCI NIH HHS R01 CA151535NHLBI NIH HHS R01 HL114093NIAID NIH HHS R01 AI044432NIAID NIH HHS R01 AI44432
6 · The paper itself

Abstract

The discovery of Ten Eleven Translocation proteins, enzymes that oxidize 5-methylcytosine (5mC) in DNA, has revealed novel mechanisms for the regulation of DNA methylation. We have mapped 5-hydroxymethylcytosine (5hmC) at different stages of T-cell development in the thymus and T-cell differentiation in the periphery. We show that 5hmC is enriched in the gene body of highly expressed genes at all developmental stages and that its presence correlates positively with gene expression. Further emphasizing the connection with gene expression, we find that 5hmC is enriched in active thymus-specific enhancers and that genes encoding key transcriptional regulators display high intragenic 5hmC levels in precursor cells at those developmental stages where they exert a positive effect. Our data constitute a valuable resource that will facilitate detailed analysis of the role of 5hmC in T-cell development and differentiation.

Indexed as

5-MethylcytosineAnimalsCell DifferentiationCell LineageCytosineDNA-Binding ProteinsDNA MethylationEnhancer Elements, GeneticFemaleGene Expression Regulation, DevelopmentalMiceMice, Inbred C57BLMice, TransgenicProto-Oncogene ProteinsT-LymphocytesT-Lymphocyte Subsets5-hydroxymethylcytosine5-MethylcytosineCytosineDNA-Binding ProteinsProto-Oncogene Proteinsepigeneticsthymic development

Identifiers

PMID25071199
PMCPMC4136618

What OpenQuestion holds

Textmetadata
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.