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

Qiling Zhou; Miao Yu; Roberto Tirado-Magallanes; Bin Li; Lingshi Kong; Mingrui Guo; Zi Hui Tan; Sanghoon Lee; Li Chai; Akihiko Numata; Touati Benoukraf; Melissa Jane Fullwood; Motomi Osato; Bing Ren; Daniel G. Tenen

doi:10.1038/s41467-020-20282-1

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

Qiling Zhou, Miao Yu, Roberto Tirado-Magallanes, Bin Li, Lingshi Kong, Mingrui Guo, Zi Hui Tan, Sanghoon Lee, Li Chai, Akihiko Numata, Touati Benoukraf, Melissa Jane Fullwood, Motomi Osato, Bing Ren, Daniel G. Tenen

Systems Biology

Research output: Contribution to journal › Article › peer-review

36 Scopus citations

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.

Original language	English (US)
Article number	43
Journal	Nature communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-20282-1
State	Published - Dec 1 2021

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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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. (2021). ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function. Nature communications, 12(1), Article 43. https://doi.org/10.1038/s41467-020-20282-1

Zhou, Q, Yu, M, Tirado-Magallanes, R, Li, B, Kong, L, Guo, M, Tan, ZH, Lee, S, Chai, L, Numata, A, Benoukraf, T, Fullwood, MJ, Osato, M, Ren, B & Tenen, DG 2021, 'ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function', Nature communications, vol. 12, no. 1, 43. https://doi.org/10.1038/s41467-020-20282-1

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

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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AU - Zhou, Qiling

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AU - Tirado-Magallanes, Roberto

AU - Li, Bin

AU - Kong, Lingshi

AU - Guo, Mingrui

AU - Tan, Zi Hui

AU - Lee, Sanghoon

AU - Chai, Li

AU - Numata, Akihiko

AU - Benoukraf, Touati

AU - Fullwood, Melissa Jane

AU - Osato, Motomi

AU - Ren, Bing

AU - Tenen, Daniel G.

PY - 2021/12/1

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N2 - 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.

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

Abstract

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