Evidence map›Paper›PMID 25271306›Full record

ArticleGenome research2015

H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells.

Agustín F Fernández, Gustavo F Bayón, Rocío G Urdinguio, Estela G Toraño, María G García, Antonella Carella, Sandra Petrus-Reurer, Cecilia Ferrero, Pablo Martinez-Camblor, Isabel Cubillo and 20 more

Erratum issuedOpen access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome research, 2015. 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 78 papers.

0numbers the graph read from it
0cells of the map it votes in
78citing 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

78 citing papers in PubMed, 153 citations in OpenAlex.

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

30 authors at 12 institutions in 7 countries.

Agustín F FernándezCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain;
Gustavo F BayónCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain;
Rocío G UrdinguioCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain;
Estela G TorañoCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain;
María G GarcíaCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain;
Antonella CarellaCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain;
Sandra Petrus-ReurerCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain;
Cecilia FerreroCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain;
Pablo Martinez-CamblorOficina de Investigación Biosanitaria (OIB-FICYT) de Asturias, 33005 Oviedo, Spain and Universidad Autónoma de Chile, Chile;
Isabel CubilloUnidad de Biotecnología Celular, Área de Genética Humana, Instituto de Salud Carlos III, 28029 Madrid, Spain;
Javier García-CastroUnidad de Biotecnología Celular, Área de Genética Humana, Instituto de Salud Carlos III, 28029 Madrid, Spain;
Jesús Delgado-CalleDepartment of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, 39011 Santander, Spain;
Flor M Pérez-CampoDepartment of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, 39011 Santander, Spain;
José A RianchoDepartment of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, 39011 Santander, Spain;
Clara BuenoJosep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, 08036 Barcelona, Spain;
Pablo MenéndezJosep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, 08036 Barcelona, Spain; Institut Català de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain;
Anouk MentinkMIRA Institute of Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands;
Katia MareschiPediatric Onco-Hematology, Stem Cell Transplantation and Cellular Therapy Division, City of Science and Health of Turin, Regina Margherita Children's Hospital, 10126 Turin, Italy; Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy;
Fabian ClaireTranslational Centre for Regenerative Medicine, University of Leipzig, 04103 Leipzig, Germany;
Corrado FagnaniGenetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy;
Emanuela MeddaGenetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy;
Virgilia ToccaceliGenetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy;
Sonia BrescianiniGenetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy;
Sebastián MoranCancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Catalonia, Spain;
Manel EstellerInstitut Català de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain; Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Catalonia, Spain;
Alexandra StolzingTranslational Centre for Regenerative Medicine, University of Leipzig, 04103 Leipzig, Germany; Loughborough University, Wolfson School of Mechanical and Manufacturing Engineering, LE11 3TU Loughborough, United Kingdom;
Jan de BoerMIRA Institute of Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands; cBITE laboratory, Merln Institute of Technology-inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands;
Lorenza NisticòGenetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy;
Maria A StaziGenetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy;
Mario F FragaCancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain; Department of Immunology and Oncology, National Center for Biotechnology, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain mffraga@cnb.csic.es affernandez@hca.es.
Universidad de Oviedo · ESIstituto Superiore di Sanità · ITUniversidad de Cantabria · ESInstitució Catalana de Recerca i Estudis Avançats · ESInstituto de Salud Carlos III · ESInstitut d'Investigació Biomédica de Bellvitge · ESJosep Carreras Leukaemia Research Institute · ESLoughborough University · GBMaastricht University · NLOspedale Regina Margherita · ITUniversity Hospital Leipzig · DEUniversity of Twente · NL

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In differentiated cells, aging is associated with hypermethylation of DNA regions enriched in repressive histone post-translational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal stem cells (MSCs) obtained from individuals aged 2 to 92 yr identified 18,735 hypermethylated and 45,407 hypomethylated CpG sites associated with aging. As in differentiated cells, hypermethylated sequences were enriched in chromatin repressive marks. Most importantly, hypomethylated CpG sites were strongly enriched in the active chromatin mark H3K4me1 in stem and differentiated cells, suggesting this is a cell type-independent chromatin signature of DNA hypomethylation during aging. Analysis of scedasticity showed that interindividual variability of DNA methylation increased during aging in MSCs and differentiated cells, providing a new avenue for the identification of DNA methylation changes over time. DNA methylation profiling of genetically identical individuals showed that both the tendency of DNA methylation changes and scedasticity depended on nongenetic as well as genetic factors. Our results indicate that the dynamics of DNA methylation during aging depend on a complex mixture of factors that include the DNA sequence, cell type, and chromatin context involved and that, depending on the locus, the changes can be modulated by genetic and/or external factors.

Indexed as

DNA MethylationAdolescentAgedAged, 80 and overAgingCell DifferentiationCells, CulturedChildChild, PreschoolChromatinDNAEpigenesis, GeneticHistonesHumansMicroarray AnalysisMiddle AgedChromatinDNAHistones

Identifiers

PMID25271306
PMCPMC4317171
OpenAlexW2110470531

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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.