Evidence map›Paper›PMID 34758327›Full record

ArticleCell reports2021

Modulating mesendoderm competence during human germ layer differentiation.

James R Valcourt, Roya E Huang, Sharmistha Kundu, Divya Venkatasubramanian, Robert E Kingston, Sharad Ramanathan

Open access · goldAbstract read
In one paragraph

Article in Cell reports, 2021. 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
1.2field-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

12 citing papers in PubMed, 22 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

6 authors at 1 institution in 1 country.

James R ValcourtSystems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Division of Applied Physics, Harvard University, Cambridge, MA 02138, USA. Electronic address: valcourt@alumni.harvard.edu.
Roya E HuangDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Division of Applied Physics, Harvard University, Cambridge, MA 02138, USA.
Sharmistha KunduDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Divya VenkatasubramanianDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Division of Applied Physics, Harvard University, Cambridge, MA 02138, USA.
Robert E KingstonDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Sharad RamanathanDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Division of Applied Physics, Harvard University, Cambridge, MA 02138, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: sharad@cgr.harvard.edu.
Harvard University · US

Funding

ROLE OF DIETARY CONSTITUENTS ON GENE EXPRESSION IN INTESTINAL EPITHELIUMP30DK040561 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI Elizabeth Austen Lawson, Takara Leah Stanley · 1994 to 2026
$31.6M
Functional Analysis of Epigenetic ComplexesR35GM131743 · NIGMS · MASSACHUSETTS GENERAL HOSPITAL · PI ROBERT KINGSTON · 2019 to 2026
$7.0M
Measuring and modeling the dynamics ofpatterning in human stem cellsR01GM131105 · NIGMS · HARVARD UNIVERSITY · PI Sharad Ramanathan · 2019 to 2026
$2.9M
NIDDK NIH HHS P30 DK040561NIGMS NIH HHS R01 GM131105NIGMS NIH HHS R35 GM131743
6 · The paper itself

Abstract

As pluripotent human embryonic stem cells progress toward one germ layer fate, they lose the ability to adopt alternative fates. Using a low-dimensional reaction coordinate to monitor progression toward ectoderm, we show that a differentiating stem cell's probability of adopting a mesendodermal fate given appropriate signals falls sharply at a point along the ectoderm trajectory. We use this reaction coordinate to prospectively isolate and profile differentiating cells based on their mesendoderm competence and analyze their RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) profiles to identify transcription factors that control the cell's mesendoderm competence. By modulating these key transcription factors, we can expand or contract the window of competence to adopt the mesendodermal fate along the ectodermal differentiation trajectory. The ability of the underlying gene regulatory network to modulate competence is essential for understanding human development and controlling the fate choices of stem cells in vitro.

Indexed as

Cell LineageGene Expression Regulation, DevelopmentalCell DifferentiationGene Expression ProfilingGene Regulatory NetworksGerm LayersHuman Embryonic Stem CellsHumansMesodermOctamer Transcription Factor-3RNA-SeqSOXB1 Transcription FactorsOctamer Transcription Factor-3POU5F1 protein, humanSOX2 protein, humanSOXB1 Transcription Factorscell fate competencedevelopmental trajectoryectodermgene regulatory networkgerm layer choicehuman embryonic stem cellsmesendodermreaction coordinatesWaddington landscape

Identifiers

PMID34758327
PMCPMC8601596
OpenAlexW3211928949

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.