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Cited by 76Gene Regulatory Network AnalysisGenomics and Chromatin DynamicsBioinformatics and Genomic Networks

Mammalian Transcription Factor Networks: Recent Advances in Interrogating Biological Complexity

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Wilkinson, Adam C., Nakauchi, Hiromitsu, Göttgens, Berthold·2017·Cell Systems
DOI 10.1016/j.cels.2017.07.004PMC PMC5928788
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Abstract

Transcription factor (TF) networks are a key determinant of cell fate decisions in mammalian development and adult tissue homeostasis and are frequently corrupted in disease. However, our inability to experimentally resolve and interrogate the complexity of mammalian TF networks has hampered the progress in this field. Recent technological advances, in particular large-scale genome-wide approaches, single-cell methodologies, live-cell imaging, and genome editing, are emerging as important technologies in TF network biology. Several recent studies even suggest a need to re-evaluate established models of mammalian TF networks. Here, we provide a brief overview of current and emerging methods to define mammalian TF networks. We also discuss how these emerging technologies facilitate new ways to interrogate complex TF networks, consider the current open questions in the field, and comment on potential future directions and biomedical applications.

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  • Core transcriptional regulatory circuitries self-sustain high expression of identity transcription factors and their target effector genes and are involved in continuous modulation of the hepatic transcriptome in response to environmental stimuli.

    “Indeed, CoRCs allows to self‐sustain high expression of identity TFs and their target effector genes in addition to being involved in the continuous modulation of the hepatic transcriptome in response to environmental stimuli (Boyer et al, 2005; Arendt et al, 2016; Wilkinson et al, 2017; Almeida et al, 2021).”

    From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Wilkinson et al, 2017

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Authors
Wilkinson, A. C., Nakauchi, H., & Göttgens, B.
Affiliations
  • Institute for Stem Cell Biology and Regenerative Medicine (US)
  • Stanford Medicine (US)
  • Wellcome/MRC Cambridge Stem Cell Institute (GB)
Corresponding author
Göttgens, Berthold
ORCID
Venue
Cell Systems
Publisher
Elsevier BV
Published
2017-10
Volume
5
Issue
4
Pages
319-331
ISSN
2405-4712 (ISSN-L)
DOI
10.1016/j.cels.2017.07.004
PMC
PMC5928788
OpenAlex
W2741314653
Cited by
76
References
27
Citations by year
2026: 7 · 2025: 6 · 2024: 8 · 2023: 16 · 2022: 5 · 2021: 11 · 2020: 8 · 2019: 14 · 2018: 1
FWCI
0.59
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Systems (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Apollo (University of Cambridge) (submittedVersion, cc-by-nc-nd)
  • Apollo
Funders
  • Bloodwise Visiting Fellowship (15050)
  • NIH-NCATS (UL1 TR001085)
  • Japan Science and Technology Agency
  • California Institute of Regenerative Medicine (LA1-06917, DISC2-08874)
  • Ludwig Foundation (12029)
  • Cancer Research UK (C1163/A12765, C1163/A21762)
  • Wellcome Trust (105031/D/14/Z, 097922/Z/11/Z)
  • MRC (MR/M008975/1)
  • NIH-NIDDK (R24 DK106766-01)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
transcriptional regulatory networks, mammalian development, tissue homeostasis, cell fate determination, single-cell transcriptomics, live-cell imaging, genome editing
MeSH terms
Gene Editing, Animals, Gene Expression Regulation, Mammals, Transcription Factors, Genome, Gene Regulatory Networks

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