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Ramachandran J, Chen W, Lex RK, Windsor KE, Lee H, Wang T, Zhou W, Ji H, Vokes SA. The BAF chromatin complex component SMARCC1 does not mediate GLI transcriptional repression of Hedgehog target genes in limb buds. Dev Biol 2023; 504:128-136. [PMID: 37805104 DOI: 10.1016/j.ydbio.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Transcriptional responses to the Hedgehog (HH) signaling pathway are primarily modulated by GLI repression in the mouse limb. Previous studies suggested a role for the BAF chromatin remodeling complex in mediating GLI repression. Consistent with this possibility, the core BAF complex protein SMARCC1 is present at most active limb enhancers including the majority of GLI enhancers. However, in contrast to GLI repression which reduces chromatin accessibility, SMARCC1 maintains chromatin accessibility at most enhancers, including those bound by GLI. Moreover, SMARCC1 binding at GLI-regulated enhancers occurs independently of GLI3. Consistent with previous studies, some individual GLI target genes are mis-regulated in Smarcc1 conditional knockouts, though most GLI target genes are unaffected. Moreover, SMARCC1 is not necessary for mediating constitutive GLI repression in HH mutant limb buds. We conclude that SMARCC1 does not mediate GLI3 repression, which we propose utilizes alternative chromatin remodeling complexes.
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Affiliation(s)
- Janani Ramachandran
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX, 78712, USA
| | - Wanlu Chen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Rachel K Lex
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kathryn E Windsor
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX, 78712, USA
| | - Hyunji Lee
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX, 78712, USA
| | - Tingchang Wang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Steven A Vokes
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX, 78712, USA.
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Ramachandran J, Chen W, Lex RK, Windsor KE, Lee H, Wang T, Zhou W, Ji H, Vokes SA. The BAF chromatin complex component SMARCC1 does not mediate GLI transcriptional repression of Hedgehog target genes in limb buds. bioRxiv 2023:2023.02.03.527038. [PMID: 36798239 PMCID: PMC9934545 DOI: 10.1101/2023.02.03.527038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Transcriptional responses to the Hedgehog (HH) signaling pathway are primarily modulated by GLI repression in the mouse limb. Previous studies suggested a role for the BAF chromatin remodeling complex in mediating GLI repression. Consistent with this possibility, the core BAF complex protein SMARCC1 is present at most active limb enhancers including the majority of GLI enhancers. However, in contrast to GLI repression which reduces chromatin accessibility, SMARCC1 maintains chromatin accessibility at most enhancers, including those bound by GLI. Moreover, SMARCC1 binding at GLI-regulated enhancers occurs independently of GLI3. Consistent with previous studies, some individual GLI target genes are mis-regulated in Smarcc1 conditional knockouts, though most GLI target genes are unaffected. Moreover, SMARCC1 is not necessary for mediating constitutive GLI repression in HH mutant limb buds. We conclude that SMARCC1 does not mediate GLI3 repression, which we propose utilizes alternative chromatin remodeling complexes.
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Affiliation(s)
- Janani Ramachandran
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street Stop A5000, Austin, TX 78712 USA
| | - Wanlu Chen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Rachel K. Lex
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street Stop A5000, Austin, TX 78712 USA
| | - Kathryn E. Windsor
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street Stop A5000, Austin, TX 78712 USA
| | - Hyunji Lee
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street Stop A5000, Austin, TX 78712 USA
| | - Tingchang Wang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Steven A. Vokes
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th Street Stop A5000, Austin, TX 78712 USA
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Lex RK, Vokes SA. Timing is everything: Transcriptional repression is not the default mode for regulating Hedgehog signaling. Bioessays 2022; 44:e2200139. [PMID: 36251875 PMCID: PMC9691524 DOI: 10.1002/bies.202200139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022]
Abstract
Hedgehog (HH) signaling is a conserved pathway that drives developmental growth and is essential for the formation of most organs. The expression of HH target genes is regulated by a dual switch mechanism where GLI proteins function as bifunctional transcriptional activators (in the presence of HH signaling) and transcriptional repressors (in the absence of HH signaling). This results in a tight control of GLI target gene expression during rapidly changing levels of pathway activity. It has long been presumed that GLI proteins also repress target genes prior to the initial expression of HH in a given tissue. This idea forms the basis for the limb bud pre-patterning model for regulating digit number. Recent findings indicate that GLI repressor proteins are indeed present prior to HH signaling but contrary to this model, GLI proteins are inert as they do not regulate transcriptional responses or enhancer chromatin modifications at this time. These findings suggest that GLI transcriptional repressor activity is not a default state as assumed, but is itself regulated in an unknown fashion. We discuss these findings and their implications for understanding pre-patterning, digit regulation, and HH-driven disease.
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Affiliation(s)
- Rachel K. Lex
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
| | - Steven A. Vokes
- Department of Molecular Bioscienc es, University of Texas at Austin, 100 E 24th Street Stop A5000, Austin, TX 78712 USA
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Lex RK, Ji Z, Falkenstein KN, Zhou W, Henry JL, Ji H, Vokes SA. GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling. eLife 2020; 9:50670. [PMID: 31989924 PMCID: PMC6986877 DOI: 10.7554/elife.50670] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/10/2020] [Indexed: 12/18/2022] Open
Abstract
Transcriptional repression needs to be rapidly reversible during embryonic development. This extends to the Hedgehog pathway, which primarily serves to counter GLI repression by processing GLI proteins into transcriptional activators. In investigating the mechanisms underlying GLI repression, we find that a subset of GLI binding regions, termed HH-responsive enhancers, specifically loses acetylation in the absence of HH signaling. These regions are highly enriched around HH target genes and primarily drive HH-specific transcriptional activity in the mouse limb bud. They also retain H3K27ac enrichment in limb buds devoid of GLI activator and repressor, indicating that their activity is primarily regulated by GLI repression. Furthermore, the Polycomb repression complex is not active at most of these regions, suggesting it is not a major mechanism of GLI repression. We propose a model for tissue-specific enhancer activity in which an HDAC-associated GLI repression complex regulates target genes by altering the acetylation status at enhancers.
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Affiliation(s)
- Rachel K Lex
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Zhicheng Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Kristin N Falkenstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Joanna L Henry
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Steven A Vokes
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
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Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA. The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription. J Biol Chem 2016; 291:7171-82. [PMID: 26797124 DOI: 10.1074/jbc.m116.714857] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Indexed: 01/20/2023] Open
Abstract
The Hedgehog (HH) signaling pathway is essential for the maintenance and response of several types of stem cells. To study the transcriptional response of stem cells to HH signaling, we searched for proteins binding to GLI proteins, the transcriptional effectors of the HH pathway in mouse embryonic stem (ES) cells. We found that both GLI3 and GLI1 bind to the pluripotency factor NANOG. The ectopic expression of NANOG inhibits GLI1-mediated transcriptional responses in a dose-dependent fashion. In differentiating ES cells, the presence of NANOG reduces the transcriptional response of cells to HH. Finally, we found thatGli1andNanogare co-expressed in ES cells at high levels. We propose that NANOG acts as a negative feedback component that provides stem cell-specific regulation of the HH pathway.
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Affiliation(s)
- Qiang Li
- From the Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, and
| | - Rachel K Lex
- From the Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, and
| | - HaeWon Chung
- From the Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, and
| | - Simone M Giovanetti
- From the Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, and
| | - Zhicheng Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Hongkai Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Maria D Person
- Institute for Cellular and Molecular Biology, and Proteomics Facility, The University of Texas, Austin, Texas 78712 and
| | - Jonghwan Kim
- From the Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, and
| | - Steven A Vokes
- From the Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, and
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