Evidence map›Paper›PMID 33770494›Full record

ArticleStem cell reports2021

Species-Specific Relationships between DNA and Chromatin Properties of CpG Islands in Embryonic Stem Cells and Differentiated Cells.

Justin Langerman, David Lopez, Matteo Pellegrini, Stephen T Smale

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

Article in Stem cell reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
0.4field-weighted citation impact, top 42% 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

6 citing papers in PubMed, 8 citations in OpenAlex.

  1. Review
  2. Article
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  6. Review
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

4 authors at 2 institutions in 1 country.

Justin LangermanDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Broad Stem Cell Research Center, University of California, Los Angeles, CA 90095, USA.
David LopezMolecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Broad Stem Cell Research Center, University of California, Los Angeles, CA 90095, USA; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Matteo PellegriniMolecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Broad Stem Cell Research Center, University of California, Los Angeles, CA 90095, USA; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Stephen T SmaleDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Broad Stem Cell Research Center, University of California, Los Angeles, CA 90095, USA. Electronic address: smale@mednet.ucla.edu.
University of California, Los Angeles · USBroad Center · US

Funding

UCLA NIGMS T32 Program AssessmentT32GM007185 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI TORRES, JORGE · 1985 to 2020
$21.7M
Roles of sumoylation and alternative polyadenylation in cellular reprogrammingP01GM099134 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI PLATH, KATHRIN · 2011 to 2021
$20.3M
Selective Regulation of Pro-Inflammatory Genes in MacrophagesR01GM086372 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SMALE, STEPHEN T · 2008 to 2015
$2.5M
NIGMS NIH HHS P01 GM099134NIGMS NIH HHS R01 GM086372NIGMS NIH HHS T32 GM007185
6 · The paper itself

Abstract

CpG islands often exhibit low DNA methylation, high histone H3 lysine 4 trimethylation, low nucleosome density, and high DNase I hypersensitivity, yet the rules by which CpG islands are sensed remain poorly understood. In this study, we first evaluated the relationships between the DNA and the chromatin properties of CpG islands in embryonic stem cells using modified bacterial artificial chromosomes. Then, using a bioinformatic approach, we identified strict CpG-island density and length thresholds in mouse embryonic stem and differentiated cells that consistently specify low DNA methylation levels. Surprisingly, the human genome exhibited a dramatically different relationship between DNA properties and DNA methylation levels of CpG islands. Further analysis allowed speculation that this difference is accommodated in part by evolutionary changes in the nucleotide composition of orthologous promoters. Thus, a change in the rules by which CpG-island properties are sensed may have co-evolved with compensatory genome adaptation events during mammalian evolution.

Indexed as

AnimalsCell DifferentiationChromatinCpG IslandsDNADNA MethylationEmbryonic DevelopmentGenome, HumanHumansMiceModels, BiologicalMouse Embryonic Stem CellsNucleotidesPromoter Regions, GeneticSpecies SpecificityChromatinDNANucleotideschromatinCpG islandsDNA methylationembryonic stem cellsepigeneticsevolutionnucleosomepromoters

Identifiers

PMID33770494
PMCPMC8072027
OpenAlexW3138241211

What OpenQuestion holds

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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.