Evidence map›Paper›PMID 26832399›Full record

ArticleCell reports2016

Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation.

Mohan Malleshaiah, Megha Padi, Pau Rué, John Quackenbush, Alfonso Martinez-Arias, Jeremy Gunawardena

Abstract read
In one paragraph

Article in Cell reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
–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

20 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Review
  8. NAC1 confines virus-specific memory formation of CD4Journal of medical virology · 2023
    Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Review
  14. Article
  15. Article
  16. Article
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  18. Article
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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.

Mohan MalleshaiahDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. Electronic address: mohan_malleshaiah@hms.harvard.edu.
Megha PadiBiostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
Pau RuéDepartment of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
John QuackenbushBiostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
Alfonso Martinez-AriasDepartment of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
Jeremy GunawardenaDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. Electronic address: jeremy_gunawardena@hms.harvard.edu.

Funding

Using Networks to Assign Gene Function in Lung DiseaseR01HL111759 · NHLBI · DANA-FARBER CANCER INST · PI QUACKENBUSH, JOHN, SILVERMAN, EDWIN K · 2012 to 2015
$3.4M
Information Processing by Post-translational ModificationR01GM105375 · NIGMS · HARVARD MEDICAL SCHOOL · PI GUNAWARDENA, JEREMY, LAHAV, GALIT · 2015 to 2022
$3.0M
Modeling phenotypic transitions in gene expression state spaceK25HG006031 · NHGRI · DANA-FARBER CANCER INST · PI PADI, MEGHA · 2011 to 2015
$890k
Canadian Institutes of Health Research 201411MFE-339075-254265NHGRI NIH HHS K25 HG006031NHGRI NIH HHS K25HG006031NHLBI NIH HHS 1R01 HL111759NHLBI NIH HHS R01 HL111759NIGMS NIH HHS R01 GM105375NIGMS NIH HHS R01GM105375
6 · The paper itself

Abstract

Pluripotent cells give rise to distinct cell types during development and are regulated by often self-reinforcing molecular networks. How such networks allow cells to differentiate is less well understood. Here, we use integrative methods to show that external signals induce reorganization of the mouse embryonic stem cell pluripotency network and that a sub-network of four factors, Nac1, Oct4, Tcf3, and Sox2, regulates their differentiation into the alternative mesendodermal and neuroectodermal fates. In the mesendodermal fate, Nac1 and Oct4 were constrained within quantitative windows, whereas Sox2 and Tcf3 were repressed. In contrast, in the neuroectodermal fate, Sox2 and Tcf3 were constrained while Nac1 and Oct4 were repressed. In addition, we show that Nac1 coordinates differentiation by activating Oct4 and inhibiting both Sox2 and Tcf3. Reorganization of progenitor cell networks around shared factors might be a common differentiation strategy and our integrative approach provides a general methodology for delineating such networks.

Indexed as

Cell DifferentiationAnimalsBase SequenceCell LineageComputational BiologyMesodermMiceMolecular Sequence DataMouse Embryonic Stem CellsNerve Tissue ProteinsNeural PlateOctamer Transcription Factor-3Pluripotent Stem CellsProtein BindingRegulatory Sequences, Nucleic AcidRepressor ProteinsNacc1 protein, mouseNerve Tissue ProteinsOctamer Transcription Factor-3Repressor ProteinsTranscription Factors

Identifiers

PMID26832399
PMCPMC4749452

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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.