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Cited by 79Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function

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Zhou, Qiling, Yu, Miao, Tirado-Magallanes, Roberto, Li, Bin, Kong, Lingshi, Guo, Mingrui, Tan, Zi Hui, Lee, Sanghoon +7 more·2021·Nature Communications
DOI 10.1038/s41467-020-20282-1PMC PMC7782510
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Abstract

CCCTC binding factor (CTCF) is an important factor in the maintenance of chromatin–chromatin interactions, yet the mechanism regulating its binding to chromatin is unknown. We demonstrate that zinc finger protein 143 (ZNF143) is a key regulator for CTCF-bound promoter–enhancer loops. In the murine genome, a large percentage of CTCF and ZNF143 DNA binding motifs are distributed 37 bp apart in the convergent orientation. Furthermore, deletion of ZNF143 leads to loss of CTCF binding on promoter and enhancer regions associated with gene expression changes. CTCF-bound promoter–enhancer loops are also disrupted after excision of ZNF143. ZNF143-CTCF-bound promoter–enhancer loops regulate gene expression patterns essential for maintenance of murine hematopoietic stem and progenitor cell integrity. Our data suggest a common feature of gene regulation is that ZNF143 is a critical factor for CTCF-bound promoter–enhancer loops.

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  • Long-term depletion of YY1 or ZNF143 in mammalian cells causes a significant reduction of enhancer-promoter loops, coupled with substantial changes in gene expression.

    “Unlike CTCF and cohesin, long-term depletion of YY1 or ZNF143 in mammalian cells causes a significant reduction of enhancer–promoter loops, coupled with substantial changes in gene expression [295, 368, 369]”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [368]

    The Results section on ZNF143 depletion reports significantly fewer promoter–enhancer loops in Znf143-deleted murine hematopoietic stem and progenitor cells; the Results section on regulated pathways reports significant gene-expression changes. This supports the ZNF143 portion of the multiply cited sentence, but this paper does not establish the stated long-term timescale or extend the finding beyond the murine cells studied. The YY1 portion is not attributed specifically to this source. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • ZNF143 binds to promoters globally and is found at the anchors of many lineage-specific enhancer-promoter loops in human and mouse cells.

    “Meanwhile, ZNF143 binds to promoters globally [367] and was found at the anchors of many lineage-specific enhancer–promoter loops in human and mouse cells [362–364, 368].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [368]

    The Results (Fig. 2; page unavailable) show ZNF143 at promoter–enhancer loop anchors in murine hematopoietic stem and progenitor cells. This source does not establish the same finding in human cells or show that the loops are lineage-specific. The separate promoter-binding clause is cited to [367], not this source. (LLM, conf=0.85)

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Cited by

Sorted by citations

Authors
Zhou, Q., Yu, M., Tirado-Magallanes, R., Li, B., Kong, L., Guo, M., Tan, Z. H., Lee, S., Chai, L., Numata, A., Benoukraf, T., Fullwood, M. J., Osato, M., Ren, B., & Tenen, D. G.
Affiliations
  • National University of Singapore (SG)
  • Fudan University (CN)
  • Ludwig Cancer Research (US)
  • The University of Texas MD Anderson Cancer Center (US)
  • Brigham and Women's Hospital (US)
  • Kyushu University (JP)
  • Memorial University of Newfoundland (CA)
  • Agency for Science, Technology and Research (SG)
  • University of California San Diego (US)
  • Harvard University (US)
Corresponding author
Tenen, Daniel G.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2021-01-04
Volume
12
Issue
1
Pages
43-43
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-020-20282-1
PMC
PMC7782510
OpenAlex
W3120635680
Cited by
79
References
14
Citations by year
2026: 7 · 2025: 13 · 2024: 14 · 2023: 9 · 2022: 29 · 2021: 7
FWCI
4.94
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • National University of Singapore (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DR-NTU (Nanyang Technological University) (submittedVersion)
Funders
  • National Research Foundation
  • National Research Foundation Singapore
  • National Institutes of Health (HL131477)
  • Medical Research Council
  • National Medical Research Council
  • Japan Society for the Promotion of Science (18K08362, 19K07668)
  • National Heart, Lung, and Blood Institute (P01HL131477)
  • National Cancer Institute (R35CA197697)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
ZNF143, CTCF, chromatin looping, hematopoietic stem cells, hematopoietic progenitor cells, zinc finger proteins, gene expression regulation, gene expression
MeSH terms
CCCTC-Binding Factor, Animals, DNA, Enhancer Elements, Genetic, Hematopoiesis, Hematopoietic Stem Cells, Mice, Inbred C57BL, Phenotype, Promoter Regions, Genetic, Protein Binding, Transcription, Genetic, Trans-Activators, Mice, Knockout, Mice, Protein Stability

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