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Cited by 119Genomics and Chromatin DynamicsBioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

A mouse tissue transcription factor atlas

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Zhou, Quan, Liu, Mingwei, Xia, Xia, Gong, Tongqing, Feng, Jinwen, Liu, Wanlin, Liu, Yang, Zhen, Bei +3 more·2017·Nature Communications
DOI 10.1038/ncomms15089PMC PMC5413951
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Abstract

Transcription factors (TFs) drive various biological processes ranging from embryonic development to carcinogenesis. Here, we employ a recently developed concatenated tandem array of consensus TF response elements (catTFRE) approach to profile the activated TFs in 24 adult and 8 fetal mouse tissues on proteome scale. A total of 941 TFs are quantitatively identified, representing over 60% of the TFs in the mouse genome. Using an integrated omics approach, we present a TF network in the major organs of the mouse, allowing data mining and generating knowledge to elucidate the roles of TFs in various biological processes, including tissue type maintenance and determining the general features of a physiological system. This study provides a landscape of TFs in mouse tissues that can be used to elucidate transcriptional regulatory specificity and programming and as a baseline that may facilitate understanding diseases that are regulated by TFs.

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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 Zhou et al, 2017

    The Results section ('TFs that maintain the tissue identity,' page unavailable) identifies Hnf4a, Hnf1a and Foxa2 as tissue-identity factors associated with hepatocytes. The liver-perturbation Results also describe six hepatocyte nuclear factors in the liver tissue-maintenance group. Our copy does not define a 13-factor hepatocyte core circuitry or establish that those factors are interconnected. (LLM, conf=0.84)

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Authors
Zhou, Q., Liu, M., Xia, X., Gong, T., Feng, J., Liu, W., Liu, Y., Zhen, B., Wang, Y., Ding, C., & Qin, J.
Affiliations
  • Beijing Proteome Research Center (CN)
  • Fudan University (CN)
  • Baylor College of Medicine (US)
Corresponding author
  • Ding, Chen
  • Qin, Jun
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2017-04-21
Volume
8
Issue
1
Pages
15089-15089
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/ncomms15089
PMC
PMC5413951
OpenAlex
W2607229512
Cited by
119
References
8
Citations by year
2026: 7 · 2025: 18 · 2024: 13 · 2023: 20 · 2022: 21 · 2021: 18 · 2020: 11 · 2019: 2 · 2018: 6 · 2017: 3
FWCI
2.46
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Cancer Prevention and Research Institute of Texas (CPRIT RP110784, RP110784)
  • National Natural Science Foundation of China (973 Program, 2016YFA0502500, 863 Program, 2014CBA02000, 2014DFB30010, 31270822, 2015AA020108)
  • National High-tech Research and Development Program (2015AA020108)
  • National Key Research and Development Program of China (2016YFA0502500, 2014CBA02000, 2015AA020108)
  • National Institute of Mental Health (U01MH105026)
Topics
  • 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
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Keywords
transcription factors, mouse tissues, transcriptional regulatory networks, tissue-specific gene regulation, fetal tissue, adult tissues, multi-omics integration
MeSH terms
Animals, Atlases as Topic, Ectoderm, Endoderm, Female, Fetus, Male, Mesoderm, Mice, Inbred C57BL, Organ Specificity, Transcription Factors, Transcription, Genetic, Genome, Gene Expression Regulation, Developmental, Response Elements, Proteome, Mice, Gene Regulatory Networks, Data Mining

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