Evidence map›Paper›PMID 20644535›Full record

ArticleNature2010

Epigenetic memory in induced pluripotent stem cells.

K Kim, A Doi, B Wen, K Ng, R Zhao, P Cahan, J Kim, M J Aryee, H Ji, L I R Ehrlich and 18 more

Abstract read
In one paragraph

Article in Nature, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,260 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1,260citing papers in PubMed, 1 pooled it
–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

1,260 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Modelling mitochondrial diseases in neuronsJournal of neuromuscular diseases · 2025
    Pooled it
  2. Article
  3. Review
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  5. Review
  6. The making of cells and organs in xenogeneic animal bioreactor.Signal transduction and targeted therapy · 2026
    Review
  7. Article
  8. Article
  9. Review
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Review
  17. Review
  18. Review
  19. Article
  20. Review

1,200 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

28 authors.

K KimStem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
A Doi
B Wen
K Ng
R Zhao
P Cahan
J Kim
M J Aryee
H Ji
L I R Ehrlich
A Yabuuchi
A Takeuchi
K C Cunniff
H Hongguang
S McKinney-Freeman
O Naveiras
T J Yoon
R A Irizarry
N Jung
J Seita
J Hanna
P Murakami
R Jaenisch
R Weissleder
S H Orkin
I L Weissman
A P Feinberg
G Q Daley

Funding

Minority Action PlanP50HG003233 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI FEINBERG, ANDREW P. · 2004 to 2013
$22.4M
Interrogation of individual cells to identify progenitors and their nichesU01HL099999 · NHLBI · STANFORD UNIVERSITY · PI WEISSMAN, IRVING L. · 2009 to 2015
$7.8M
In Vitro Reprogramming of Somatic Cells into Pluripotent ES-like CellsR37HD045022 · NICHD · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI JAENISCH, RUDOLF · 2009 to 2017
$7.5M
HSC Diversity: Regulation by Clonal Selection vs Epigenetic InductionR01CA086065 · NCI · STANFORD UNIVERSITY · PI WEISSMAN, IRVING L. · 2000 to 2017
$6.9M
Preprocessing and Analysis Tools for High-Throughput TechnologiesR01GM083084 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI IRIZARRY, RAFAEL ANGEL · 2007 to 2018
$4.4M
NIH Director's Pioneer Award (RMI)DP1OD000256 · OD · CHILDREN'S HOSPITAL BOSTON · PI DALEY, GEORGE Q · 2004 to 2008
$4.2M
BWS and Embryonal Tumor Suppressor Genes on 11p15R37CA054358 · NCI · JOHNS HOPKINS UNIVERSITY · PI FEINBERG, ANDREW P. · 2001 to 2009
$4.0M
Murine Models for Regenerative MedicineR01DK070055 · NIDDK · CHILDREN'S HOSPITAL BOSTON · PI DALEY, GEORGE Q · 2005 to 2009
$3.5M
Comparative phenotypic, functional, and molecular analysis of ESC and iPSCRC2HL102815 · NHLBI · BOSTON CHILDREN'S HOSPITAL · PI CHURCH, GEORGE M, COLLINS, JAMES J · 2009 to 2010
$3.4M
Hematopoietic stem cells from totipotent stem cell typesR01DK059279 · NIDDK · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI DALEY, GEORGE Q · 2001 to 2009
$3.3M
THYMIC LYMPHOCYTE DEVELOPMENTR01AI047457 · NIAID · STANFORD UNIVERSITY · PI WEISSMAN, IRVING LERNER · 2000 to 2004
$1.6M
BIOLOGY AND TRANSPLANTATION OF CLPR01AI047458 · NIAID · STANFORD UNIVERSITY · PI WEISSMAN, IRVING LERNER · 2001 to 2005
$1.5M
Howard Hughes Medical InstituteNCI NIH HHS CA86065NCI NIH HHS R01 CA086065NCI NIH HHS R37 CA054358NCI NIH HHS R37CA054358NHGRI NIH HHS P50 HG003233NHGRI NIH HHS P50HG003233NHLBI NIH HHS HL099999NHLBI NIH HHS K99 HL093212NHLBI NIH HHS K99HL093212-01NHLBI NIH HHS RC2 HL102815NHLBI NIH HHS RC2-HL102815NHLBI NIH HHS U01 HL099999NIAID NIH HHS R01 AI047457NIAID NIH HHS R01AI047457NIAID NIH HHS R01 AI047458NIAID NIH HHS R01AI047458NICHD NIH HHS R37 HD045022NIDDK NIH HHS R01 DK059279NIDDK NIH HHS R01 DK070055NIDDK NIH HHS R01-DK59279NIDDK NIH HHS R01-DK70055NIGMS NIH HHS R01 GM083084NIH HHS DP1 OD000256
6 · The paper itself

Abstract

Somatic cell nuclear transfer and transcription-factor-based reprogramming revert adult cells to an embryonic state, and yield pluripotent stem cells that can generate all tissues. Through different mechanisms and kinetics, these two reprogramming methods reset genomic methylation, an epigenetic modification of DNA that influences gene expression, leading us to hypothesize that the resulting pluripotent stem cells might have different properties. Here we observe that low-passage induced pluripotent stem cells (iPSCs) derived by factor-based reprogramming of adult murine tissues harbour residual DNA methylation signatures characteristic of their somatic tissue of origin, which favours their differentiation along lineages related to the donor cell, while restricting alternative cell fates. Such an 'epigenetic memory' of the donor tissue could be reset by differentiation and serial reprogramming, or by treatment of iPSCs with chromatin-modifying drugs. In contrast, the differentiation and methylation of nuclear-transfer-derived pluripotent stem cells were more similar to classical embryonic stem cells than were iPSCs. Our data indicate that nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin that may influence efforts at directed differentiation for applications in disease modelling or treatment.

Indexed as

Epigenesis, GeneticAnimalsCell DifferentiationCell LineageCellular ReprogrammingDNA MethylationEmbryonic Stem CellsGenomeHematopoietic Stem CellsInduced Pluripotent Stem CellsMiceMice, Inbred C57BLMice, Inbred CBANuclear Transfer TechniquesTranscription FactorsTranscription Factors

Identifiers

PMID20644535
PMCPMC3150836

What OpenQuestion holds

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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.