Evidence map›Paper›PMID 38194345›Full record

ArticleCell reports2024

Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells.

Matthew M Edwards, Ning Wang, Dashiell J Massey, Sakshi Bhatele, Dieter Egli, Amnon Koren

Open access · goldAbstract read
In one paragraph

Article in Cell reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
1.4field-weighted citation impact, top 21% of its field
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

8 citing papers in PubMed, 6 citations in OpenAlex.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

6 authors at 3 institutions in 1 country.

Matthew M EdwardsDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Ning WangDepartment of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
Dashiell J MasseyDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Sakshi BhateleDepartment of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
Dieter EgliDepartment of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA. Electronic address: de2220@columbia.edu.
Amnon KorenDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA. Electronic address: amnon.koren@roswellpark.org.
New York Stem Cell Foundation · USCornell University · USRoswell Park Comprehensive Cancer Center · US

Funding

The Genetic Basis of Human DNA Replication TimingR35GM148071 · NIGMS · ROSWELL PARK CANCER INSTITUTE CORP · PI Amnon Koren · 2023 to 2026
$1.5M
NIGMS NIH HHS R35 GM148071
6 · The paper itself

Abstract

Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.

Indexed as

Induced Pluripotent Stem CellsCell DifferentiationCellular ReprogrammingDNA MethylationDNA Replication TimingCP: Molecular biologyCP: Stem cell researchDNA replication timingepigenetic aberrationsheterochromatininduced pluripotent stem cellssomatic cell nuclear transferstem cell differentiation

Identifiers

PMID38194345
PMCPMC11231959
OpenAlexW4390661277

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.