Evidence map›Paper›PMID 30240614›Full record

ArticleiScience2018

Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming.

Sijia Liu, Haiming Chen, Scott Ronquist, Laura Seaman, Nicholas Ceglia, Walter Meixner, Pin-Yu Chen, Gerald Higgins, Pierre Baldi, Steve Smale and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in iScience, 2018. 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. Review
  2. Article
  3. Article
  4. Dynamic sensor selection for biomarker discovery.Proceedings of the National Academy of Sciences of the United States of America · 2025
    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

13 authors.

Sijia LiuDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
Haiming ChenDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Scott RonquistDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Laura SeamanDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Nicholas CegliaDepartment of Computer Science, University of California-Irvine, Irvine, CA 92697, USA.
Walter MeixnerDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Pin-Yu ChenAI Foundations, IBM T. J. Watson Research Center, Yorktown Heights, NY 10598, USA.
Gerald HigginsDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Pierre BaldiDepartment of Computer Science, University of California-Irvine, Irvine, CA 92697, USA.
Steve SmaleDepartment of Mathematics, City University of Hong Kong, Hong Kong 999077, China; Department of Mathematics, University of California, Berkeley, CA 94720, USA.
Alfred HeroDepartment of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
Lindsey A MuirDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Indika RajapakseDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: indikar@umich.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming.

Indexed as

Integrative Aspects of Cell BiologyMolecular StructureOmicsSystems Biology

Identifiers

PMID30240614
PMCPMC6137960

What OpenQuestion holds

Textmetadata
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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.