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Cited by 45Genomics and Chromatin DynamicsLiver physiology and pathologyDevelopmental Biology and Gene Regulation

Transcription Control of Liver Development

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Tachmatzidi, Evangelia C., Galanopoulou, Ourania, Talianidis, Iannis·2021·Cells
DOI 10.3390/cells10082026PMC PMC8391549
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Abstract

During liver organogenesis, cellular transcriptional profiles are constantly reshaped by the action of hepatic transcriptional regulators, including FoxA1-3, GATA4/6, HNF1α/β, HNF4α, HNF6, OC-2, C/EBPα/β, Hex, and Prox1. These factors are crucial for the activation of hepatic genes that, in the context of compact chromatin, cannot access their targets. The initial opening of highly condensed chromatin is executed by a special class of transcription factors known as pioneer factors. They bind and destabilize highly condensed chromatin and facilitate access to other “non-pioneer” factors. The association of target genes with pioneer and non-pioneer transcription factors takes place long before gene activation. In this way, the underlying gene regulatory regions are marked for future activation. The process is called “bookmarking”, which confers transcriptional competence on target genes. Developmental bookmarking is accompanied by a dynamic maturation process, which prepares the genomic loci for stable and efficient transcription. Stable hepatic expression profiles are maintained during development and adulthood by the constant availability of the main regulators. This is achieved by a self-sustaining regulatory network that is established by complex cross-regulatory interactions between the major regulators. This network gradually grows during liver development and provides an epigenetic memory mechanism for safeguarding the optimal expression of the regulators.

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  • Besides Hep-ID transcription factors and an additional set of cell-specific transcription factors with well-characterized hepatic functions (Nr1i3/Car, Rorc/Rorg, Hnf1a, and Gata4), the majority of transcription factors from cluster G belonged to cell-type enriched or ubiquitous transcription factors.

    “This further highlighted that, besides Hep‐ID TFs and an additional set of cell‐specific TFs with well characterized hepatic functions (Nr1i3/Car, Rorc/Rorg, Hnf1a and Gata4; Tachmatzidi et al, 2021), the majority of TFs from cluster G belonged to CTE or UBQ TFs (Fig 1J and Dataset EV1).”

    From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Tachmatzidi et al, 2021

    The GATA Family section describes GATA4’s role in liver-bud expansion, and the HNF1 section states that HNF1α regulates genes critical for liver function. The cited paper does not establish hepatic functions for Nr1i3/Car or Rorc/Rorg, so it supports only part of the cited list. The cluster-G classification is presented as the citing authors’ own result, not as a finding attributed to this source. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • Hepatocyte identity is typically defined as relying on a handful of interconnected hepatocyte-specific core transcriptional regulatory circuitry transcription factors (Hep-ID TFs) including HNF4A, FOXA, and NR1H4 (FXR).

    “hepatocyte identity is typically defined as relying on a handful of interconnected hepatocyte‐specific CoRC TFs (hereafter called Hep‐ID TFs) including HNF4A, FOXA or NR1H4 (FXR; Tachmatzidi et al, 2021).”

    From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Tachmatzidi et al, 2021

    Section 14, “Maintenance of Stable Hepatic Gene Expression Patterns” (page not provided), describes an interconnected core of hepatic transcription factors that includes HNF4α and FoxA2. It does not include NR1H4 (FXR) in that core, so the cited paper supports the general circuitry claim but not the full list attributed to it. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Hep-ID transcription factors comprise the well-accepted and thoroughly experimentally verified drivers of hepatocyte identity.

    “Hep‐ID TFs comprise the well‐accepted and thoroughly experimentally verified drivers of hepatocyte identity (Reizel et al, 2020; Tachmatzidi et al, 2021).”

    From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Tachmatzidi et al, 2021

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Authors
Tachmatzidi, E. C., Galanopoulou, O., & Talianidis, I.
Affiliations
  • University of Crete (GR)
  • FORTH Institute of Molecular Biology and Biotechnology (GR)
Corresponding author
Talianidis, Iannis
ORCID
Talianidis, Iannis
Venue
Cells
Publisher
MDPI AG
Published
2021-08-08
Volume
10
Issue
8
Pages
2026
ISSN
2073-4409 (ISSN-L)
DOI
10.3390/cells10082026
PMC
PMC8391549
OpenAlex
W3190463137
Cited by
45
References
194
Citations by year
2026: 8 · 2025: 11 · 2024: 9 · 2023: 7 · 2022: 10
FWCI
0.68
Type
journal article
Language
en
Open access
Licence
Locations
  • Cells (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • AXA Research Fund (T1EDK-00407)
  • Hellenic Foundation for Research and Innovation (10444 - 10442)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Health Sciences › Medicine › Hepatology › Liver physiology and pathology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
liver development, liver organogenesis, chromatin accessibility, pioneer transcription factors, bookmarking, chromatin condensation, HNF4α, HNF6, Hex, Prox1, epigenetic memory, transcriptional regulatory networks, hepatic gene expression
MeSH terms
Animals, Cell Differentiation, Endoderm, Humans, Liver, Stem Cells, Transcription Factors, Gene Expression Regulation, Developmental, Hepatocytes, Organogenesis

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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