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Cited by 172Pluripotent Stem Cells ResearchGenomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

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D’Alessio, Ana C., Fan, Zi Peng, Wert, Katherine J., Baranov, Petr, Cohen, Malkiel A., Saini, Janmeet S., Cohick, Evan, Charniga, Carol +7 more·2015·Stem Cell Reports
DOI 10.1016/j.stemcr.2015.09.016PMC PMC4649293
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Abstract

Hundreds of transcription factors (TFs) are expressed in each cell type, but cell identity can be induced through the activity of just a small number of core TFs. Systematic identification of these core TFs for a wide variety of cell types is currently lacking and would establish a foundation for understanding the transcriptional control of cell identity in development, disease, and cell-based therapy. Here, we describe a computational approach that generates an atlas of candidate core TFs for a broad spectrum of human cells. The potential impact of the atlas was demonstrated via cellular reprogramming efforts where candidate core TFs proved capable of converting human fibroblasts to retinal pigment epithelial-like cells. These results suggest that candidate core TFs from the atlas will prove a useful starting point for studying transcriptional control of cell identity and reprogramming in many human cell types.

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  • The hepatocyte core transcriptional regulatory circuitry comprises 13 Hep-ID transcription factors commonly defined in different studies as interconnected hepatocyte-specific transcription factors.

    “We defined the hepatocyte CoRC as a set of 13 Hep‐ID TFs commonly defined in different studies as interconnected hepatocyte‐specific TFs (Kyrmizi et al, 2006; D'Alessio Ana et al, 2015; Zhou et al, 2017; Dubois et al, 2020a; Dataset EV1).”

    From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as D'Alessio Ana et al, 2015

    The Results (page unavailable) say the atlas includes candidate core transcription factors for hepatocytes, with overlap with factors used in hepatocyte reprogramming. The paper does not define a 13-factor Hep-ID set or establish that those factors form an interconnected hepatocyte-specific circuitry; it focuses on the ten top-scoring factors per cell type as primary candidates. (LLM, conf=0.85)

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Authors
D’Alessio, A. C., Fan, Z. P., Wert, K. J., Baranov, P., Cohen, M. A., Saini, J. S., Cohick, E., Charniga, C., Dadon, D., Hannett, N. M., Young, M. J., Temple, S., Jaenisch, R., Lee, T. I., & Young, R. A.
Affiliations
  • Whitehead Institute for Biomedical Research (US)
  • Massachusetts Eye and Ear Infirmary (US)
  • University at Albany, State University of New York (US)
  • Neural Stem Cell Institute (US)
Corresponding author
  • Lee, Tong Ihn
  • Young, Richard A.
ORCID
Venue
Stem Cell Reports
Publisher
Elsevier BV
Published
2015-11
Volume
5
Issue
5
Pages
763-775
ISSN
2213-6711 (ISSN-L)
DOI
10.1016/j.stemcr.2015.09.016
PMC
PMC4649293
OpenAlex
W1810920534
Cited by
172
References
7
Citations by year
2026: 7 · 2025: 7 · 2024: 19 · 2023: 14 · 2022: 22 · 2021: 22 · 2020: 18 · 2019: 14 · 2018: 15 · 2017: 18 · 2016: 15
FWCI
6.94
Type
journal article
Language
en
Open access
Licence
Locations
  • Stem Cell Reports (publishedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
Funders
  • National Institutes of Health
  • National Human Genome Research Institute (HG002668, R01HG002668)
  • National Cancer Institute (CA146445, R01CA146445)
  • National Institute of Neurological Disorders and Stroke (R01NS088538)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
transcription factors, cell identity, transcriptional atlas, cellular reprogramming, transcriptional regulation, human cell types
MeSH terms
Cell Line, Computer Simulation, Epithelial Cells, Fibroblasts, Humans, Transcription Factors, Retinal Pigment Epithelium, Cellular Reprogramming

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