Evidence map›Paper›PMID 30577748›Full record

ArticleBMC genomics2018

Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming.

Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Stephen T Smale, Kenneth S Zaret, Kathrin Plath, Matteo Pellegrini

Open access · goldAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
1.0field-weighted citation impact, top 23% 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

12 citing papers in PubMed, 23 citations in OpenAlex.

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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

9 authors at 4 institutions in 2 countries.

Kai FuDepartment of Molecular, Cellular and Developmental Biology, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Constantinos ChronisDavid Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Abdenour SoufiInstitute for Regenerative Medicine and Epigenetics Program, Department of Cell and Developmental Biology, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
Giancarlo BonoraDepartment of Molecular, Cellular and Developmental Biology, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Miguel EdwardsDepartment of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Stephen T SmaleDepartment of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Kenneth S ZaretInstitute for Regenerative Medicine and Epigenetics Program, Department of Cell and Developmental Biology, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
Kathrin PlathDavid Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Matteo PellegriniDepartment of Molecular, Cellular and Developmental Biology, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, 90095, USA. matteope@gmail.com.
University of California, Los Angeles · USBroad Center · USTranslational Therapeutics (United States) · USUniversity of Pennsylvania · US

Funding

Roles of sumoylation and alternative polyadenylation in cellular reprogrammingP01GM099134 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI PLATH, KATHRIN · 2011 to 2021
$20.3M
Biotechnology and Biological Sciences Research Council BB/M018040/1Medical Research Council MR/N024028/1NIGMS NIH HHS P01 GM099134NIH HHS 5P01GM099134
6 · The paper itself

Abstract

backgroundBoth human and mouse fibroblasts can be reprogrammed to pluripotency with Oct4, Sox2, Klf4, and c-Myc (OSKM) transcription factors. While both systems generate pluripotency, human reprogramming takes considerably longer than mouse.

resultsTo assess additional similarities and differences, we sought to compare the binding of the reprogramming factors between the two systems. In human fibroblasts, the OSK factors initially target many more closed chromatin sites compared to mouse. Despite this difference, the intra- and intergenic distribution of target sites, target genes, primary binding motifs, and combinatorial binding patterns between the reprogramming factors are largely shared. However, while many OSKM binding events in early mouse cell reprogramming occur in syntenic regions, only a limited number is conserved in human.

conclusionsOur findings suggest similar general effects of OSKM binding across these two species, even though the detailed regulatory networks have diverged significantly.

Indexed as

AnimalsCells, CulturedCellular ReprogrammingChromatinFibroblastsHumansInduced Pluripotent Stem CellsKruppel-Like Factor 4Kruppel-Like Transcription FactorsMiceOctamer Transcription Factor-3Proto-Oncogene Proteins c-mycSOXB1 Transcription FactorsSpecies SpecificityTranscription FactorsChromatinKLF4 protein, humanKlf4 protein, mouseKruppel-Like Factor 4Kruppel-Like Transcription FactorsOctamer Transcription Factor-3Proto-Oncogene Proteins c-mycSOXB1 Transcription FactorsTranscription FactorsComparative epigenomicsiPS cellsReprogramming

Identifiers

PMID30577748
PMCPMC6303873
OpenAlexW2905798439

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.