FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function

Yeqing A. Yang; Jonathan C. Zhao; Ka Wing Fong; Jung Kim; Shangze Li; Chunxiao Song; Bing Song; Bin Zheng; Chuan He; Jindan Yu

doi:10.1093/nar/gkw498

FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function

Yeqing A. Yang, Jonathan C. Zhao, Ka Wing Fong, Jung Kim, Shangze Li, Chunxiao Song, Bing Song, Bin Zheng, Chuan He, Jindan Yu

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

43 Scopus citations

Abstract

Forkhead box A1 (FOXA1) is an FKHD family protein that plays pioneering roles in lineage-specific enhancer activation and gene transcription. Through genome-wide location analyses, here we show that FOXA1 expression and occupancy are, in turn, required for the maintenance of these epigenetic signatures, namely DNA hypomethylation and histone 3 lysine 4 methylation. Mechanistically, this involves TET1, a 5-methylcytosine dioxygenase. We found that FOXA1 induces TET1 expression via direct binding to its cis-regulatory elements. Further, FOXA1 physically interacts with the TET1 protein through its CXXC domain. TET1 thus co-occupies FOXA1-dependent enhancers and mediates local DNA demethylation and concomitant histone 3 lysine 4 methylation, further potentiating FOXA1 recruitment. Consequently, FOXA1 binding events are markedly reduced following TET1 depletion. Together, our results suggest that FOXA1 is not only able to recognize but also remodel the epigenetic signatures at lineage-specific enhancers, which is mediated, at least in part, by a feed-forward regulatory loop between FOXA1 and TET1.

Original language	English
Pages (from-to)	8153-8164
Number of pages	12
Journal	Nucleic Acids Research
Volume	44
Issue number	17
DOIs	https://doi.org/10.1093/nar/gkw498
State	Published - Sep 30 2016

Bibliographical note

Funding Information:
U.S. Department of Defense [W81XWH-13-1-0319 to J.Y., in part]; American Cancer Society Research Scholar Award [RSG-12-085-01 to J.Y.]; National Institutes of Health [R01HG006827 to C.H.]; Howard Hughes Medical Institute (to C.H.); NIH/NCI training grant [T32 CA09560 to Y.A.Y., in part]; NIH Training Program in Oncogenesis and Developmental Biology [T32 CA080621 to J.K., in part]. Funding for open access charge: National Institutes of Health [R01-CA172384 to J.Y.]. Conflict of interest statement. None declared.

Publisher Copyright:
© 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkw498

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title = "FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function",

abstract = "Forkhead box A1 (FOXA1) is an FKHD family protein that plays pioneering roles in lineage-specific enhancer activation and gene transcription. Through genome-wide location analyses, here we show that FOXA1 expression and occupancy are, in turn, required for the maintenance of these epigenetic signatures, namely DNA hypomethylation and histone 3 lysine 4 methylation. Mechanistically, this involves TET1, a 5-methylcytosine dioxygenase. We found that FOXA1 induces TET1 expression via direct binding to its cis-regulatory elements. Further, FOXA1 physically interacts with the TET1 protein through its CXXC domain. TET1 thus co-occupies FOXA1-dependent enhancers and mediates local DNA demethylation and concomitant histone 3 lysine 4 methylation, further potentiating FOXA1 recruitment. Consequently, FOXA1 binding events are markedly reduced following TET1 depletion. Together, our results suggest that FOXA1 is not only able to recognize but also remodel the epigenetic signatures at lineage-specific enhancers, which is mediated, at least in part, by a feed-forward regulatory loop between FOXA1 and TET1.",

author = "Yang, {Yeqing A.} and Zhao, {Jonathan C.} and Fong, {Ka Wing} and Jung Kim and Shangze Li and Chunxiao Song and Bing Song and Bin Zheng and Chuan He and Jindan Yu",

note = "Funding Information: U.S. Department of Defense [W81XWH-13-1-0319 to J.Y., in part]; American Cancer Society Research Scholar Award [RSG-12-085-01 to J.Y.]; National Institutes of Health [R01HG006827 to C.H.]; Howard Hughes Medical Institute (to C.H.); NIH/NCI training grant [T32 CA09560 to Y.A.Y., in part]; NIH Training Program in Oncogenesis and Developmental Biology [T32 CA080621 to J.K., in part]. Funding for open access charge: National Institutes of Health [R01-CA172384 to J.Y.]. Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.",

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AU - Zhao, Jonathan C.

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AU - Song, Chunxiao

AU - Song, Bing

AU - Zheng, Bin

AU - He, Chuan

AU - Yu, Jindan

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PY - 2016/9/30

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N2 - Forkhead box A1 (FOXA1) is an FKHD family protein that plays pioneering roles in lineage-specific enhancer activation and gene transcription. Through genome-wide location analyses, here we show that FOXA1 expression and occupancy are, in turn, required for the maintenance of these epigenetic signatures, namely DNA hypomethylation and histone 3 lysine 4 methylation. Mechanistically, this involves TET1, a 5-methylcytosine dioxygenase. We found that FOXA1 induces TET1 expression via direct binding to its cis-regulatory elements. Further, FOXA1 physically interacts with the TET1 protein through its CXXC domain. TET1 thus co-occupies FOXA1-dependent enhancers and mediates local DNA demethylation and concomitant histone 3 lysine 4 methylation, further potentiating FOXA1 recruitment. Consequently, FOXA1 binding events are markedly reduced following TET1 depletion. Together, our results suggest that FOXA1 is not only able to recognize but also remodel the epigenetic signatures at lineage-specific enhancers, which is mediated, at least in part, by a feed-forward regulatory loop between FOXA1 and TET1.

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FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function

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