Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud

Naoko Koyano-Nakagawa; Wuming Gong; Satyabrata Das; Joshua Theisen; Tran B. Swanholm; Daniel V Ly; Nikita Dsouza; Bhairab N Singh; Hiroko Kawakami; Samantha Young; Katherine Q. Chen; Yasu Kawakami; Daniel J Garry

doi:10.1038/s41467-022-31848-6

Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud

Naoko Koyano-Nakagawa, Wuming Gong, Satyabrata Das, Joshua Theisen, Tran B. Swanholm, Daniel V Ly, Nikita Dsouza, Bhairab N Singh, Hiroko Kawakami, Samantha Young, Katherine Q. Chen, Yasu Kawakami, Daniel J Garry

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

2 Scopus citations

Abstract

Sonic hedgehog (Shh) is essential for limb development, and the mechanisms that govern the propagation and maintenance of its expression has been well studied; however, the mechanisms that govern the initiation of Shh expression are incomplete. Here we report that ETV2 initiates Shh expression by changing the chromatin status of the developmental limb enhancer, ZRS. Etv2 expression precedes Shh in limb buds, and Etv2 inactivation prevents the opening of limb chromatin, including the ZRS, resulting in an absence of Shh expression. Etv2 overexpression in limb buds causes nucleosomal displacement at the ZRS, ectopic Shh expression, and polydactyly. Areas of nucleosome displacement coincide with ETS binding site clusters. ETV2 also functions as a transcriptional activator of ZRS and is antagonized by ETV4/5 repressors. Known human polydactyl mutations introduce novel ETV2 binding sites in the ZRS, suggesting that ETV2 dosage regulates ZRS activation. These studies identify ETV2 as a pioneer transcription factor (TF) regulating the onset of Shh expression, having both a chromatin regulatory role and a transcriptional activation role.

Original language	English (US)
Article number	4221
Journal	Nature communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-31848-6
State	Published - Dec 2022

Bibliographical note

Funding Information:
This work was supported by the NIH (1U01HL134764 to DJG, 5U01HL100407 to DJG, and R01AR064195 to YK). We are grateful to Drs. Chi-chung Hui, Juan Carlos Izpisua Belmonte, Michael Roberts, Dennis K. Watson, Vincenzo Zappavigna, Yasushi Nakagawa, and Rolf Zeller for sharing plasmids and equipment. The authors acknowledge Mark Sanders, Sandra Wagner, Debra Kulhanek, Erik Skie, Pruthvi Shah, Lars Meisner, and Akiko Nakagawa for technical assistance. The authors acknowledge the efforts of Cynthia Faraday for figure preparation.

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© 2022, The Author(s).

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@article{d006ade44faf42c59e7a1b84f909866d,

title = "Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud",

abstract = "Sonic hedgehog (Shh) is essential for limb development, and the mechanisms that govern the propagation and maintenance of its expression has been well studied; however, the mechanisms that govern the initiation of Shh expression are incomplete. Here we report that ETV2 initiates Shh expression by changing the chromatin status of the developmental limb enhancer, ZRS. Etv2 expression precedes Shh in limb buds, and Etv2 inactivation prevents the opening of limb chromatin, including the ZRS, resulting in an absence of Shh expression. Etv2 overexpression in limb buds causes nucleosomal displacement at the ZRS, ectopic Shh expression, and polydactyly. Areas of nucleosome displacement coincide with ETS binding site clusters. ETV2 also functions as a transcriptional activator of ZRS and is antagonized by ETV4/5 repressors. Known human polydactyl mutations introduce novel ETV2 binding sites in the ZRS, suggesting that ETV2 dosage regulates ZRS activation. These studies identify ETV2 as a pioneer transcription factor (TF) regulating the onset of Shh expression, having both a chromatin regulatory role and a transcriptional activation role.",

author = "Naoko Koyano-Nakagawa and Wuming Gong and Satyabrata Das and Joshua Theisen and Swanholm, {Tran B.} and Ly, {Daniel V} and Nikita Dsouza and Singh, {Bhairab N} and Hiroko Kawakami and Samantha Young and Chen, {Katherine Q.} and Yasu Kawakami and Garry, {Daniel J}",

note = "Funding Information: This work was supported by the NIH (1U01HL134764 to DJG, 5U01HL100407 to DJG, and R01AR064195 to YK). We are grateful to Drs. Chi-chung Hui, Juan Carlos Izpisua Belmonte, Michael Roberts, Dennis K. Watson, Vincenzo Zappavigna, Yasushi Nakagawa, and Rolf Zeller for sharing plasmids and equipment. The authors acknowledge Mark Sanders, Sandra Wagner, Debra Kulhanek, Erik Skie, Pruthvi Shah, Lars Meisner, and Akiko Nakagawa for technical assistance. The authors acknowledge the efforts of Cynthia Faraday for figure preparation. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1038/s41467-022-31848-6",

language = "English (US)",

volume = "13",

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T1 - Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud

AU - Koyano-Nakagawa, Naoko

AU - Gong, Wuming

AU - Das, Satyabrata

AU - Theisen, Joshua

AU - Swanholm, Tran B.

AU - Ly, Daniel V

AU - Dsouza, Nikita

AU - Singh, Bhairab N

AU - Kawakami, Hiroko

AU - Young, Samantha

AU - Chen, Katherine Q.

AU - Kawakami, Yasu

AU - Garry, Daniel J

N1 - Funding Information: This work was supported by the NIH (1U01HL134764 to DJG, 5U01HL100407 to DJG, and R01AR064195 to YK). We are grateful to Drs. Chi-chung Hui, Juan Carlos Izpisua Belmonte, Michael Roberts, Dennis K. Watson, Vincenzo Zappavigna, Yasushi Nakagawa, and Rolf Zeller for sharing plasmids and equipment. The authors acknowledge Mark Sanders, Sandra Wagner, Debra Kulhanek, Erik Skie, Pruthvi Shah, Lars Meisner, and Akiko Nakagawa for technical assistance. The authors acknowledge the efforts of Cynthia Faraday for figure preparation. Publisher Copyright: © 2022, The Author(s).

PY - 2022/12

Y1 - 2022/12

N2 - Sonic hedgehog (Shh) is essential for limb development, and the mechanisms that govern the propagation and maintenance of its expression has been well studied; however, the mechanisms that govern the initiation of Shh expression are incomplete. Here we report that ETV2 initiates Shh expression by changing the chromatin status of the developmental limb enhancer, ZRS. Etv2 expression precedes Shh in limb buds, and Etv2 inactivation prevents the opening of limb chromatin, including the ZRS, resulting in an absence of Shh expression. Etv2 overexpression in limb buds causes nucleosomal displacement at the ZRS, ectopic Shh expression, and polydactyly. Areas of nucleosome displacement coincide with ETS binding site clusters. ETV2 also functions as a transcriptional activator of ZRS and is antagonized by ETV4/5 repressors. Known human polydactyl mutations introduce novel ETV2 binding sites in the ZRS, suggesting that ETV2 dosage regulates ZRS activation. These studies identify ETV2 as a pioneer transcription factor (TF) regulating the onset of Shh expression, having both a chromatin regulatory role and a transcriptional activation role.

AB - Sonic hedgehog (Shh) is essential for limb development, and the mechanisms that govern the propagation and maintenance of its expression has been well studied; however, the mechanisms that govern the initiation of Shh expression are incomplete. Here we report that ETV2 initiates Shh expression by changing the chromatin status of the developmental limb enhancer, ZRS. Etv2 expression precedes Shh in limb buds, and Etv2 inactivation prevents the opening of limb chromatin, including the ZRS, resulting in an absence of Shh expression. Etv2 overexpression in limb buds causes nucleosomal displacement at the ZRS, ectopic Shh expression, and polydactyly. Areas of nucleosome displacement coincide with ETS binding site clusters. ETV2 also functions as a transcriptional activator of ZRS and is antagonized by ETV4/5 repressors. Known human polydactyl mutations introduce novel ETV2 binding sites in the ZRS, suggesting that ETV2 dosage regulates ZRS activation. These studies identify ETV2 as a pioneer transcription factor (TF) regulating the onset of Shh expression, having both a chromatin regulatory role and a transcriptional activation role.

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JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 4221

ER -

Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud

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Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud

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