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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] [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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2
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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3
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George A, Lee J, Liu J, Kim S, Brooks BP. Zebrafish model of RERE syndrome recapitulates key ophthalmic defects that are rescued by small molecule inhibitor of shh signaling. Dev Dyn 2022; 252:495-509. [PMID: 36576487 DOI: 10.1002/dvdy.561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 12/02/2022] [Accepted: 12/12/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND RERE is a highly conserved transcriptional co-regulator that is associated with a human neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH, OMIM: 616975). RESULTS We show that the zebrafish rerea mutant (babyface) robustly recapitulates optic fissure closure defects resulting from loss of RERE function, as observed in humans. These defects result from expansion of proximal retinal optic stalk (OS) and reduced expression of some of the ventral retinal fate genes due to deregulated protein signaling. Using zebrafish and cell-based assays, we determined that NEDBEH-associated human RERE variants function as hypomorphs in their ability to repress shh signaling and some exhibit abnormal nuclear localization. Inhibiting shh signaling by the protein inhibitor HPI-1 rescues coloboma, confirming our observation that coloboma in rerea mutants is indeed due to deregulation of shh signaling. CONCLUSIONS Zebrafish rerea mutants exhibit OS and optic fissure closure defects. The optic fissure closure defect was rescued by an shh signaling inhibitor, suggesting that this defect could arise due to deregulated shh signaling.
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Affiliation(s)
- Aman George
- Pediatric Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jerry Lee
- Pediatric Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - James Liu
- Pediatric Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Suzie Kim
- Pediatric Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Brian P Brooks
- Pediatric Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, 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] [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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He T, Fan Y, Wang Y, Liu M, Zhu AJ. Dissection of the microRNA Network Regulating Hedgehog Signaling in Drosophila. Front Cell Dev Biol 2022; 10:866491. [PMID: 35573695 PMCID: PMC9096565 DOI: 10.3389/fcell.2022.866491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
The evolutionarily conserved Hedgehog (Hh) signaling plays a critical role in embryogenesis and adult tissue homeostasis. Aberrant Hh signaling often leads to various forms of developmental anomalies and cancer. Since altered microRNA (miRNA) expression is associated with developmental defects and tumorigenesis, it is not surprising that several miRNAs have been found to regulate Hh signaling. However, these miRNAs are mainly identified through small-scale in vivo screening or in vitro assays. As miRNAs preferentially reduce target gene expression via the 3' untranslated region, we analyzed the effect of reduced expression of core components of the Hh signaling cascade on downstream signaling activity, and generated a transgenic Drosophila toolbox of in vivo miRNA sensors for core components of Hh signaling, including hh, patched (ptc), smoothened (smo), costal 2 (cos2), fused (fu), Suppressor of fused (Su(fu)), and cubitus interruptus (ci). With these tools in hand, we performed a genome-wide in vivo miRNA overexpression screen in the developing Drosophila wing imaginal disc. Of the twelve miRNAs identified, seven were not previously reported in the in vivo Hh regulatory network. Moreover, these miRNAs may act as general regulators of Hh signaling, as their overexpression disrupts Hh signaling-mediated cyst stem cell maintenance during spermatogenesis. To identify direct targets of these newly discovered miRNAs, we used the miRNA sensor toolbox to show that miR-10 and miR-958 directly target fu and smo, respectively, while the other five miRNAs act through yet-to-be-identified targets other than the seven core components of Hh signaling described above. Importantly, through loss-of-function analysis, we found that endogenous miR-10 and miR-958 target fu and smo, respectively, whereas deletion of the other five miRNAs leads to altered expression of Hh signaling components, suggesting that these seven newly discovered miRNAs regulate Hh signaling in vivo. Given the powerful effects of these miRNAs on Hh signaling, we believe that identifying their bona fide targets of the other five miRNAs will help reveal important new players in the Hh regulatory network.
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Affiliation(s)
- Tao He
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yu Fan
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Yao Wang
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Min Liu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Alan Jian Zhu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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6
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GLI transcriptional repression is inert prior to Hedgehog pathway activation. Nat Commun 2022; 13:808. [PMID: 35145123 PMCID: PMC8831537 DOI: 10.1038/s41467-022-28485-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/28/2022] [Indexed: 12/28/2022] Open
Abstract
The Hedgehog (HH) pathway regulates a spectrum of developmental processes through the transcriptional mediation of GLI proteins. GLI repressors control tissue patterning by preventing sub-threshold activation of HH target genes, presumably even before HH induction, while lack of GLI repression activates most targets. Despite GLI repression being central to HH regulation, it is unknown when it first becomes established in HH-responsive tissues. Here, we investigate whether GLI3 prevents precocious gene expression during limb development. Contrary to current dogma, we find that GLI3 is inert prior to HH signaling. While GLI3 binds to most targets, loss of Gli3 does not increase target gene expression, enhancer acetylation or accessibility, as it does post-HH signaling. Furthermore, GLI repression is established independently of HH signaling, but after its onset. Collectively, these surprising results challenge current GLI pre-patterning models and demonstrate that GLI repression is not a default state for the HH pathway. GLI repression has been presumed to be the default transcriptional state and important for pre-patterning tissues. Challenging current models, the authors show that GLI3 repression is inert in the limb bud before the onset of Hedgehog signaling.
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7
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Zhou M, Jiang J. Gli Phosphorylation Code in Hedgehog Signal Transduction. Front Cell Dev Biol 2022; 10:846927. [PMID: 35186941 PMCID: PMC8855225 DOI: 10.3389/fcell.2022.846927] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Hedgehog (Hh) family of secreted proteins governs many key processes in embryonic development and adult tissue homeostasis in species ranging from insects to human. Deregulation of Hh signaling has been implicated in a wide range of human diseases including birth defect and cancer. Hh signaling pathway culminates in the conversion of the latent transcription factor Cubitus interruptus (Ci)/Gli from a repressor form (CiR/GliR) into an activator form (CiA/GliA). Both the production of CiR/GliR in the absence of Hh and the formation of CiA/GliA in response to Hh are regulated by phosphorylation. Whereas previous studies demonstrated that sequential phosphorylation by protein kinase A (PKA), glycogen synthase kinase 3 (GSK3), and casein kinase 1 (CK1) at multiple Ser/Thr clusters in the C-terminal region of Ci/Gli targets it for proteolytic processing to generate CiR/GliR, recent studies revealed that phosphorylation of Ci/Gli by the Fused (Fu)/Unc-51 like kinase (Ulk) family kinases Fu/Ulk3/Stk36 and other kinases contributes to Ci/Gli activation. Fu/Ulk3/Stk36-mediated phosphorylation of Ci/Gli is stimulated by Hh, leading to altered interaction between Ci/Gli and the Hh pathway repressor Sufu. Here we review our current understanding of how various Ci/Gli phosphorylation events are regulated and how they influence Hh signal transduction.
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Affiliation(s)
- Mengmeng Zhou
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Jin Jiang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, United States.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, United States
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8
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Li G, Zhao H, Guo H, Wang Y, Cui X, Xu B, Guo X. Functional and transcriptomic analyses of the NF-Y family provide insights into the defense mechanisms of honeybees under adverse circumstances. Cell Mol Life Sci 2020; 77:4977-4995. [PMID: 32016487 PMCID: PMC11104996 DOI: 10.1007/s00018-019-03447-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 12/02/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023]
Abstract
As predominant pollinators, honeybees are important for crop production and terrestrial ecosystems. Recently, various environmental stresses have led to large declines in honeybee populations in many regions. The ability of honeybees to respond to these stresses is critical for their survival. However, the details of the stress defense mechanisms of honeybees have remained elusive. Here, we found that the Nuclear Factor Y (NF-Y) family (containing NF-YA, NF-YB, and NF-YC) is a novel stress mediator family that regulates honeybee environmental stress resistance. NF-YA localized in the nucleus, NF-YB accumulated in the cytoplasm, and NF-YC presented in both the nucleus and cytoplasm. NF-YC interacted with NF-YA and NF-YB in vitro and in vivo, and the nuclear import of NF-YB relied on its interaction with NF-YC. We further found that the expression of NF-Y was induced under multiple stress conditions. In addition, NF-Y regulated many stress responses and antioxidant genes at the transcriptome-wide level, and knockdown of NF-Y repressed the expression of stress-inducible genes, particularly LOC108003540 and LOC107994062, under adverse circumstances. Silencing NF-Y lowered honeybee stress resistance by reducing total antioxidant capacity and enhancing oxidative impairment. Collectively, these results indicate that NF-Y plays important roles in stress responses. Our study sheds light on the underlying defense mechanisms of honeybees under environmental stress.
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Affiliation(s)
- Guilin Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Hang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Hongbin Guo
- Statistics Department, University of Auckland, 38 Princes Street, Auckland, New Zealand
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Xuepei Cui
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
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9
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Das P, Bhadra MP. Histone deacetylase (Rpd3) regulates Drosophila early brain development via regulation of Tailless. Open Biol 2020; 10:200029. [PMID: 32873153 PMCID: PMC7536075 DOI: 10.1098/rsob.200029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/29/2020] [Indexed: 11/29/2022] Open
Abstract
Tailless is a committed transcriptional repressor and principal regulator of the brain and eye development in Drosophila. Rpd3, the histone deacetylase, is an established repressor that interacts with co-repressors like Sin3a, Prospero, Brakeless and Atrophin. This study aims at deciphering the role of Rpd3 in embryonic segmentation and larval brain development in Drosophila. It delineates the mechanism of Tailless regulation by Rpd3, along with its interacting partners. There was a significant reduction in Tailless in Rpd3 heteroallelic mutant embryos, substantiating that Rpd3 is indispensable for the normal Tailless expression. The expression of the primary readout, Tailless was correlative to the expression of the neural cell adhesion molecule homologue, Fascilin2 (Fas2). Rpd3 also aids in the proper development of the mushroom body. Both Tailless and Fas2 expression are reported to be antagonistic to the epidermal growth factor receptor (EGFR) expression. The decrease in Tailless and Fas2 expression highlights that EGFR is upregulated in the larval mutants, hindering brain development. This study outlines the axis comprising Rpd3, dEGFR, Tailless and Fas2, which interact to fine-tune the early segmentation and larval brain development. Therefore, Rpd3 along with Tailless has immense significance in early embryogenesis and development of the larval brain.
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Affiliation(s)
- Paromita Das
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR) Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai 600 113, India
| | - Manika Pal Bhadra
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR) Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai 600 113, India
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Sanna S, Esposito S, Masala A, Sini P, Nieddu G, Galioto M, Fais M, Iaccarino C, Cestra G, Crosio C. HDAC1 inhibition ameliorates TDP-43-induced cell death in vitro and in vivo. Cell Death Dis 2020; 11:369. [PMID: 32409664 PMCID: PMC7224392 DOI: 10.1038/s41419-020-2580-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
TDP-43 pathology is a disease hallmark that characterizes both amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP). TDP-43 undergoes several posttranslational modifications that can change its biological activities and its aggregative propensity, which is a common hallmark of different neurodegenerative conditions. New evidence is provided by the current study pointing at TDP-43 acetylation in ALS cellular models. Using both in vitro and in vivo approaches, we demonstrate that TDP-43 interacts with histone deacetylase 1 (HDAC1) via RRM1 and RRM2 domains, that are known to contain the two major TDP-43 acetylation sites, K142 and K192. Moreover, we show that TDP-43 is a direct transcriptional activator of CHOP promoter and this activity is regulated by acetylation. Finally and most importantly, we observe both in cell culture and in Drosophila that a HDCA1 reduced level (genomic inactivation or siRNA) or treatment with pan-HDAC inhibitors exert a protective role against WT or pathological mutant TDP-43 toxicity, suggesting TDP-43 acetylation as a new potential therapeutic target. HDAC inhibition efficacy in neurodegeneration has long been debated, but future investigations are warranted in this area. Selection of more specific HDAC inhibitors is still a promising option for neuronal protection especially as HDAC1 appears as a downstream target of both TDP- 43 and FUS, another ALS-related gene.
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Affiliation(s)
- Simona Sanna
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Sonia Esposito
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Alessandra Masala
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Paola Sini
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Gabriele Nieddu
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Manuela Galioto
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Milena Fais
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Gianluca Cestra
- Istitute of Molecular Biology and Pathology-National Research Council at Department of Biology and Biotechnology-Charles Darwin, Sapienza University of Rome, P.Le A.Moro 5, I-00185, Rome, Italy
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy.
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11
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Li G, Zhao H, Guo H, Wang Y, Cui X, Li H, Xu B, Guo X. Analyses of the function of DnaJ family proteins reveal an underlying regulatory mechanism of heat tolerance in honeybee. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:137036. [PMID: 32059293 DOI: 10.1016/j.scitotenv.2020.137036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
There is clear evidence of severe honeybee declines in recent years, and parallel declines of plant community and crop productivity that rely on them. Different stresses, including heat stress, are among the primary drivers of this decline. However, the mechanisms by which honeybees respond to heat stress are elusive. Though heat shock proteins (Hsps) play important roles in heat stress response, the function of DnaJs (a subfamily of Hsps) is unclear. Here, we aimed to determine the underlying regulatory mechanism of honeybees to heat stress mediated by DnaJs. We found that several DnaJ genes, including DnaJA1, DnaJB12 and DnaJC8, are key for honeybee heat tolerance. DnaJA1 and DnaJB12 are cytoplasmic proteins, and DnaJC8 is a nuclear protein. The expression of DnaJA1, DnaJB12 and DnaJC8 was induced at different levels under short-term and long-term heat stress. Phenotypic analysis indicated that DnaJA1, DnaJB12 and DnaJC8 knockdown attenuated honeybee heat resistance. In addition, DnaJA1 participated in the heat stress response by upregulating many heat-inducible genes at the transcriptome-wide level, especially LOC108002668 and LOC107995148. Importantly, the upregulation of LOC108002668 and LOC107995148 was significantly repressed under heat stress when DnaJA1 was knocked down. We also found that knockdown of DnaJA1, DnaJB12 and DnaJC8 decreased antioxidant defense ability and increased the degree of oxidative damage in the honeybee. Taken together, our results indicate that DnaJ genes play important roles under heat stress in the honeybee. Overexpression of DnaJ genes may protect honeybees from heat stress-induced injuries and increase their survival rate.
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Affiliation(s)
- Guilin Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Hang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Hongbin Guo
- Statistics Department, University of Auckland, 38 Princes Street, Auckland, New Zealand
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Xuepei Cui
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Han Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China.
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12
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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] [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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13
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Kopp Z, Park Y. Longer lifespan in the Rpd3 and Loco signaling results from the reduced catabolism in young age with noncoding RNA. Aging (Albany NY) 2019; 11:230-239. [PMID: 30620723 PMCID: PMC6339784 DOI: 10.18632/aging.101744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/22/2018] [Indexed: 11/25/2022]
Abstract
Downregulation of Rpd3 (histone deacetylase) or Loco (regulator of G-protein signaling protein) extends Drosophila lifespan with higher stress resistance. We found rpd3-downregulated long-lived flies genetically interact with loco-upregulated short-lived flies in stress resistance and lifespan. Gene expression profiles between those flies revealed that they regulate common target genes in metabolic enzymes and signaling pathways, showing an opposite expression pattern in their contrasting lifespans. Functional analyses of more significantly changed genes indicated that the activities of catabolic enzymes and uptake/storage proteins are reduced in long-lived flies with Rpd3 downregulation. This reduced catabolism exhibited from a young age is considered to be necessary for the resultant longer lifespan of the Rpd3- and Loco-downregulated old flies, which mimics the dietary restriction (DR) effect that extends lifespan in the several species. Inversely, those catabolic activities that break down carbohydrates, lipids, and peptides were high in the short lifespan of Loco-upregulated flies. Long noncoding gene, dntRL (CR45923), was also found as a putative target modulated by Rpd3 and Loco for the longevity. Interestingly, this dntRL could affect stress resistance and lifespan, suggesting that the dntRL lncRNA may be involved in the metabolic mechanism of Rpd3 and Loco signaling.
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Affiliation(s)
- Zachary Kopp
- Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark, NJ 07103, USA
| | - Yongkyu Park
- Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark, NJ 07103, USA
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14
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Cheng Y, Chen D. Fruit fly research in China. J Genet Genomics 2018; 45:583-592. [PMID: 30455037 DOI: 10.1016/j.jgg.2018.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/21/2018] [Accepted: 09/29/2018] [Indexed: 11/19/2022]
Abstract
Served as a model organism over a century, fruit fly has significantly pushed forward the development of global scientific research, including in China. The high similarity in genomic features between fruit fly and human enables this tiny insect to benefit the biomedical studies of human diseases. In the past decades, Chinese biologists have used fruit fly to make numerous achievements on understanding the fundamental questions in many diverse areas of biology. Here, we review some of the recent fruit fly studies in China, and mainly focus on those studies in the fields of stem cell biology, cancer therapy and regeneration medicine, neurological disorders and epigenetics.
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Affiliation(s)
- Ying Cheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dahua Chen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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15
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Lv X, Chen H, Zhang S, Zhang Z, Pan C, Xia Y, Fan J, Wu W, Lu Y, Zhang L, Wu H, Zhao Y. Fsh-Pc-Sce complex mediates active transcription of Cubitus interruptus (Ci). J Mol Cell Biol 2018; 10:437-447. [PMID: 29432547 DOI: 10.1093/jmcb/mjy008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/07/2018] [Indexed: 12/30/2022] Open
Abstract
The Hedgehog (Hh) signaling pathway plays important roles in both embryonic development and adult tissue homeostasis. Such biological functions are mediated by the transcription factor Cubitus interruptus (Ci). Yet the transcriptional regulation of the effector Ci itself is poorly investigated. Through an RNAi-based genetic screen, we identified that female sterile (1) homeotic (Fsh), a transcription co-activator, directly activates Ci transcription. Biochemistry assays demonstrated physical interactions among Fsh, Sex combs extra (Sce), and Polycomb (Pc). Functional assays further showed that both Pc and Sce are required for Ci expression, which is not likely mediated by the derepression of Engrailed (En), a repressor of Ci, in Pc or Sce mutant cells. Finally, we provide evidence showing that Pc/Sce facilitates the binding of Fsh at Ci locus and that the physical interaction between Fsh and Pc is essential for Fsh-mediated Ci transcription. Taken together, we not only uncover that Ci is transcriptionally regulated by Fsh-Pc-Sce complex but also provide evidence for the coordination between Fsh and PcG proteins in transcriptional regulation.
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Affiliation(s)
- Xiangdong Lv
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Hao Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Shuo Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhao Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Chenyu Pan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuanxin Xia
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jialin Fan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenqing Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Lu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hailong Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yun Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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16
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Hu Y, Schmitt-Engel C, Schwirz J, Stroehlein N, Richter T, Majumdar U, Bucher G. A morphological novelty evolved by co-option of a reduced gene regulatory network and gene recruitment in a beetle. Proc Biol Sci 2018; 285:rspb.2018.1373. [PMID: 30135167 DOI: 10.1098/rspb.2018.1373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/25/2018] [Indexed: 12/18/2022] Open
Abstract
The mechanisms underlying the evolution of morphological novelties have remained enigmatic but co-option of existing gene regulatory networks (GRNs), recruitment of genes and the evolution of orphan genes have all been suggested to contribute. Here, we study a morphological novelty of beetle pupae called gin-trap. By combining the classical candidate gene approach with unbiased screening in the beetle Tribolium castaneum, we find that 70% of the tested components of the wing network were required for gin-trap development. However, many downstream and even upstream components were not included in the co-opted network. Only one gene was recruited from another biological context, but it was essential for the anteroposterior symmetry of the gin-traps, which represents a gin-trap-unique morphological innovation. Our data highlight the importance of co-option and modification of GRNs. The recruitment of single genes may not be frequent in the evolution of morphological novelties, but may be essential for subsequent diversification of the novelties. Finally, after having screened about 28% of annotated genes in the Tribolium genome to identify the genes required for gin-trap development, we found none of them are orphan genes, suggesting that orphan genes may have played only a minor, if any, role in the evolution of gin-traps.
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Affiliation(s)
- Yonggang Hu
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Christian Schmitt-Engel
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Jonas Schwirz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Nadi Stroehlein
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Tobias Richter
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Upalparna Majumdar
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
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17
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Li G, Zhang Y, Ni Y, Wang Y, Xu B, Guo X. Identification of a melatonin receptor type 1A gene (AccMTNR1A) in Apis cerana cerana and its possible involvement in the response to low temperature stress. Naturwissenschaften 2018; 105:24. [DOI: 10.1007/s00114-018-1546-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 12/20/2022]
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18
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Wang Z, Lyu J, Wang F, Miao C, Nan Z, Zhang J, Xi Y, Zhou Q, Yang X, Ge W. The histone deacetylase HDAC1 positively regulates Notch signaling during Drosophila wing development. Biol Open 2018; 7:bio.029637. [PMID: 29437043 PMCID: PMC5861358 DOI: 10.1242/bio.029637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The Notch signaling pathway is highly conserved across different animal species and plays crucial roles in development and physiology. Regulation of Notch signaling occurs at multiple levels in different tissues and cell types. Here, we show that the histone deacetylase HDAC1 acts as a positive regulator of Notch signaling during Drosophila wing development. Depletion of HDAC1 causes wing notches on the margin of adult wing. Consistently, the expression of Notch target genes is reduced in the absence of HDAC1 during wing margin formation. We further provide evidence that HDAC1 acts upstream of Notch activation. Mechanistically, we show that HDAC1 regulates Notch protein levels by promoting Notch transcription. Consistent with this, the HDAC1-associated transcriptional co-repressor Atrophin (Atro) is also required for transcriptional activation of Notch in the wing disc. In summary, our results demonstrate that HDAC1 positively regulates Notch signaling and reveal a previously unidentified function of HDAC1 in Notch signaling.
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Affiliation(s)
- Zehua Wang
- Division of Human Reproduction and Developmental Genetics, The Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jialan Lyu
- Division of Human Reproduction and Developmental Genetics, The Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Fang Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Chen Miao
- Division of Human Reproduction and Developmental Genetics, The Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zi Nan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiayu Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yongmei Xi
- Division of Human Reproduction and Developmental Genetics, The Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qi Zhou
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaohang Yang
- Division of Human Reproduction and Developmental Genetics, The Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, The Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China .,Institute of Genetics and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
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19
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Kacsoh BZ, Greene CS, Bosco G. Machine Learning Analysis Identifies Drosophila Grunge/Atrophin as an Important Learning and Memory Gene Required for Memory Retention and Social Learning. G3 (BETHESDA, MD.) 2017; 7:3705-3718. [PMID: 28889104 PMCID: PMC5677163 DOI: 10.1534/g3.117.300172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022]
Abstract
High-throughput experiments are becoming increasingly common, and scientists must balance hypothesis-driven experiments with genome-wide data acquisition. We sought to predict novel genes involved in Drosophila learning and long-term memory from existing public high-throughput data. We performed an analysis using PILGRM, which analyzes public gene expression compendia using machine learning. We evaluated the top prediction alongside genes involved in learning and memory in IMP, an interface for functional relationship networks. We identified Grunge/Atrophin (Gug/Atro), a transcriptional repressor, histone deacetylase, as our top candidate. We find, through multiple, distinct assays, that Gug has an active role as a modulator of memory retention in the fly and its function is required in the adult mushroom body. Depletion of Gug specifically in neurons of the adult mushroom body, after cell division and neuronal development is complete, suggests that Gug function is important for memory retention through regulation of neuronal activity, and not by altering neurodevelopment. Our study provides a previously uncharacterized role for Gug as a possible regulator of neuronal plasticity at the interface of memory retention and memory extinction.
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Affiliation(s)
- Balint Z Kacsoh
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Giovanni Bosco
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
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20
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Pan C, Xiong Y, Lv X, Xia Y, Zhang S, Chen H, Fan J, Wu W, Liu F, Wu H, Zhou Z, Zhang L, Zhao Y. UbcD1 regulates Hedgehog signaling by directly modulating Ci ubiquitination and processing. EMBO Rep 2017; 18:1922-1934. [PMID: 28887318 PMCID: PMC5666607 DOI: 10.15252/embr.201643289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 07/31/2017] [Accepted: 08/10/2017] [Indexed: 01/20/2023] Open
Abstract
The Hh pathway controls many morphogenetic processes in metazoans and plays important roles in numerous pathologies and in cancer. Hh signaling is mediated by the activity of the Gli/Ci family of transcription factors. Several studies in Drosophila have shown that ubiquitination by the ubiquitin E3 ligases Slimb and Rdx(Hib) plays a crucial role in controlling Ci stability dependent on the levels of Hh signals. If Hh levels are low, Slimb adds K11- and K48-linked poly-ubiquitin chains on Ci resulting in partial degradation. Ubiquitin E2 enzymes are pivotal in determining the topologies of ubiquitin chains. However, which E2 enzymes participate in the selective ubiquitination-degradation of Ci remains elusive. Here, we find that the E2 enzyme UbcD1 negatively regulates Hh signaling activity in Drosophila wing disks. Genetic and biochemical analyses in wing disks and in cultured cells reveal that UbcD1 directly controls Ci stability. Interestingly, UbcD1 is found to be selectively involved in Slimb-mediated Ci degradation. Finally, we show that the homologs of UbcD1 play a conserved role in modulating Hh signaling in vertebrates.
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Affiliation(s)
- Chenyu Pan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yue Xiong
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiangdong Lv
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuanxin Xia
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Shuo Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Hao Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jialin Fan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenqing Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hailong Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhaocai Zhou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yun Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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21
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Selvan N, Williamson R, Mariappa D, Campbell DG, Gourlay R, Ferenbach AT, Aristotelous T, Hopkins-Navratilova I, Trost M, van Aalten DMF. A mutant O-GlcNAcase enriches Drosophila developmental regulators. Nat Chem Biol 2017; 13:882-887. [PMID: 28604694 DOI: 10.1038/nchembio.2404] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 03/14/2017] [Indexed: 01/09/2023]
Abstract
Protein O-GlcNAcylation is a reversible post-translational modification of serines and threonines on nucleocytoplasmic proteins. It is cycled by the enzymes O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (O-GlcNAcase or OGA). Genetic approaches in model organisms have revealed that protein O-GlcNAcylation is essential for early embryogenesis. The Drosophila melanogaster gene supersex combs (sxc), which encodes OGT, is a polycomb gene, whose null mutants display homeotic transformations and die at the pharate adult stage. However, the identities of the O-GlcNAcylated proteins involved and the underlying mechanisms linking these phenotypes to embryonic development are poorly understood. Identification of O-GlcNAcylated proteins from biological samples is hampered by the low stoichiometry of this modification and by limited enrichment tools. Using a catalytically inactive bacterial O-GlcNAcase mutant as a substrate trap, we have enriched the O-GlcNAc proteome of the developing Drosophila embryo, identifying, among others, known regulators of Hox genes as candidate conveyors of OGT function during embryonic development.
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Affiliation(s)
- Nithya Selvan
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Ritchie Williamson
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Daniel Mariappa
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - David G Campbell
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Robert Gourlay
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Tonia Aristotelous
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Iva Hopkins-Navratilova
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK
| | - Daan M F van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
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22
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Yeung K, Boija A, Karlsson E, Holmqvist PH, Tsatskis Y, Nisoli I, Yap D, Lorzadeh A, Moksa M, Hirst M, Aparicio S, Fanto M, Stenberg P, Mannervik M, McNeill H. Atrophin controls developmental signaling pathways via interactions with Trithorax-like. eLife 2017; 6:e23084. [PMID: 28327288 PMCID: PMC5409829 DOI: 10.7554/elife.23084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/15/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro's critical role in development and disease, relatively little is known about Atro's binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways. We show that Atro regulates Dpp and Notch signaling in larval imaginal discs, at least partially via regulation of thickveins and fringe. In addition, bioinformatics analyses, sequential ChIP and coimmunoprecipitation experiments reveal that Atro interacts with the Drosophila GAGA Factor, Trithorax-like (Trl), and they bind to the same loci simultaneously. Phenotypic analyses of Trl and Atro clones suggest that Atro is required to modulate the transcription activation by Trl in larval imaginal discs. Taken together, these data indicate that Atro is a major Trl cofactor that functions to moderate developmental gene transcription.
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Affiliation(s)
- Kelvin Yeung
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ann Boija
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Edvin Karlsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden
| | - Per-Henrik Holmqvist
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Yonit Tsatskis
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ilaria Nisoli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Damian Yap
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Alireza Lorzadeh
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Manolis Fanto
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Helen McNeill
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
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Zhang T, Sheng Z, Du W. Loss of histone deacetylase HDAC1 induces cell death in Drosophila epithelial cells through JNK and Hippo signaling. Mech Dev 2016; 141:4-13. [PMID: 27378074 DOI: 10.1016/j.mod.2016.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/15/2016] [Accepted: 07/01/2016] [Indexed: 12/18/2022]
Abstract
Inactivation of HDAC1 and its homolog HDAC2 or addition of HDAC inhibitors in mammalian systems induces apoptosis, cell cycle arrest, and developmental defects. Although these phenotypes have been extensively characterized, the precise underlying mechanisms remain unclear, particularly in in vivo settings. In this study, we show that inactivation of Rpd3, the only HDAC1 and HDAC2 ortholog in Drosophila, induced apoptosis and clone elimination in the developing eye and wing imaginal discs. Depletion of Rpd3 by RNAi cell-autonomously increased JNK activities and decreased activities of Yki, the nuclear effecter of Hippo signaling pathway. In addition, inhibition of JNK activities largely rescued Rpd3 RNAi-induced apoptosis, but did not affect its inhibition of Yki activities. Conversely, increasing the Yki activities largely rescued Rpd3 RNAi-induced apoptosis, but did not affect its induction of JNK activities. Furthermore, inactivation of Mi-2, a core component of the Rpd3-containing NuRD complex strongly induced JNK activities; while inactivation of Sin3A, a key component of the Rpd3-containing Sin3 complex, significantly inhibited Yki activities. Taken together, these results reveal that inactivation of Rpd3 independently regulates JNK and Yki activities and that both Hippo and JNK signaling pathways contribute to Rpd3 RNAi-induced apoptosis.
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Affiliation(s)
- Tianyi Zhang
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Zhentao Sheng
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Wei Du
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA.
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24
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Kuleesha Y, Puah WC, Wasser M. Live imaging of muscle histolysis in Drosophila metamorphosis. BMC DEVELOPMENTAL BIOLOGY 2016; 16:12. [PMID: 27141974 PMCID: PMC4855724 DOI: 10.1186/s12861-016-0113-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/26/2016] [Indexed: 11/23/2022]
Abstract
Background The contribution of programmed cell death (PCD) to muscle wasting disorders remains a matter of debate. Drosophila melanogaster metamorphosis offers the opportunity to study muscle cell death in the context of development. Using live cell imaging of the abdomen, two groups of larval muscles can be observed, doomed muscles that undergo histolysis and persistent muscles that are remodelled and survive into adulthood. Method To identify and characterize genes that control the decision between survival and cell death of muscles, we developed a method comprising in vivo imaging, targeted gene perturbation and time-lapse image analysis. Our approach enabled us to study the cytological and temporal aspects of abnormal cell death phenotypes. Results In a previous genetic screen for genes controlling muscle size and cell death in metamorphosis, we identified gene perturbations that induced cell death of persistent or inhibit histolysis of doomed larval muscles. RNA interference (RNAi) of the genes encoding the helicase Rm62 and the lysosomal Cathepsin-L homolog Cysteine proteinase 1 (Cp1) caused premature cell death of persistent muscle in early and mid-pupation, respectively. Silencing of the transcriptional co-repressor Atrophin inhibited histolysis of doomed muscles. Overexpression of dominant-negative Target of Rapamycin (TOR) delayed the histolysis of a subset of doomed and induced ablation of all persistent muscles. RNAi of AMPKα, which encodes a subunit of the AMPK protein complex that senses AMP and promotes ATP formation, led to loss of attachment and a spherical morphology. None of the perturbations affected the survival of newly formed adult muscles, suggesting that the method is useful to find genes that are crucial for the survival of metabolically challenged muscles, like those undergoing atrophy. The ablation of persistent muscles did not affect eclosion of adult flies. Conclusions Live imaging is a versatile approach to uncover gene functions that are required for the survival of muscle undergoing remodelling, yet are dispensable for other adult muscles. Our approach promises to identify molecular mechanisms that can explain the resilience of muscles to PCD. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0113-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yadav Kuleesha
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.,School of Computer Engineering, Nanyang Technological University, N4-2A-05, Nanyang Avenue, Singapore, 639798, Republic of Singapore
| | - Wee Choo Puah
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Martin Wasser
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore. .,Present address: BioImagingMW, Block 28D Dover Crescent, #31-73, Singapore, 134028, Republic of Singapore.
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25
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Deubiquitination of Ci/Gli by Usp7/HAUSP Regulates Hedgehog Signaling. Dev Cell 2015; 34:58-72. [PMID: 26120032 DOI: 10.1016/j.devcel.2015.05.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/18/2015] [Accepted: 05/19/2015] [Indexed: 01/20/2023]
Abstract
Hedgehog (Hh) signaling plays essential roles in animal development and tissue homeostasis, and its misregulation causes congenital diseases and cancers. Regulation of the ubiquitin/proteasome-mediated proteolysis of Ci/Gli transcription factors is central to Hh signaling, but whether deubiquitinase is involved in this process remains unknown. Here, we show that Hh stimulates the binding of a ubiquitin-specific protease Usp7 to Ci, which positively regulates Hh signaling activity through inhibiting Ci ubiquitination and degradation mediated by both Slimb-Cul1 and Hib-Cul3 E3 ligases. Furthermore, we find that Usp7 forms a complex with GMP-synthetase (GMPS) to promote Hh pathway activity. Finally, we show that the mammalian counterpart of Usp7, HAUSP, positively regulates Hh signaling by modulating Gli ubiquitination and stability. Our findings reveal a conserved mechanism by which Ci/Gli is stabilized by a deubiquitination enzyme and identify Usp7/HUASP as a critical regulator of Hh signaling and potential therapeutic target for Hh-related cancers.
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26
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Xiong Y, Liu C, Zhao Y. Decoding Ci: from partial degradation to inhibition. Dev Growth Differ 2014; 57:98-108. [PMID: 25495033 DOI: 10.1111/dgd.12187] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 11/28/2022]
Abstract
Hedgehog is a morphogen, which is widely involved in the regulation of cell proliferation, differentiation and tissue patterning during development in both vertebrate and invertebrate, such as in coordination of eye, brain, gonad, gut and tracheal development. In invertebrate, Cubitus interruptus (Ci) modification process is the last identified step before transcriptional activation in the Hh signaling pathway. Ci can form a truncated repressor (Ci(R) /Ci75) or act as an activator (Ci(A) /Ci155) based on Hh gradient to regulate the expressions of target genes. The activity of Ci is mediated by different mechanisms, including processing, trafficking and degradation. While in vertebrate, Glioblastomas (Glis), homologs of Ci, play similar but more complex roles in the regulation of mammals Hh pathway. Hh signaling is responsible for a wide variety of processes during embryonic development and adult tissue homeostasis. Malfunction of Hh signaling could cause various diseases including birth defects and cancers. Enormous efforts were made in the past decades to explore the Hh pathway regulation and the results have provided us important insights into disease diagnosis and therapeutic treatment. In this review, we focus on a small branch of Hh pathway regulation based on studies in the Drosophila system, mainly about Ci degradation, aiming to explain how Ci is modified by different ubiquitin ligases due to the strong or moderate Hh signals and then been subjected to complete or partial degradation by proteasomes. Overall, we intend to offer an overview on how Ci responds to and relays Hh signals in a precise manner to control target genes expressions and ensures proper Hh signal transduction.
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Affiliation(s)
- Yue Xiong
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
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27
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Aberger F, Ruiz i Altaba A. Context-dependent signal integration by the GLI code: the oncogenic load, pathways, modifiers and implications for cancer therapy. Semin Cell Dev Biol 2014; 33:93-104. [PMID: 24852887 PMCID: PMC4151135 DOI: 10.1016/j.semcdb.2014.05.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/12/2014] [Indexed: 01/10/2023]
Abstract
Canonical Hedgehog (HH) signaling leads to the regulation of the GLI code: the sum of all positive and negative functions of all GLI proteins. In humans, the three GLI factors encode context-dependent activities with GLI1 being mostly an activator and GLI3 often a repressor. Modulation of GLI activity occurs at multiple levels, including by co-factors and by direct modification of GLI structure. Surprisingly, the GLI proteins, and thus the GLI code, is also regulated by multiple inputs beyond HH signaling. In normal development and homeostasis these include a multitude of signaling pathways that regulate proto-oncogenes, which boost positive GLI function, as well as tumor suppressors, which restrict positive GLI activity. In cancer, the acquisition of oncogenic mutations and the loss of tumor suppressors - the oncogenic load - regulates the GLI code toward progressively more activating states. The fine and reversible balance of GLI activating GLI(A) and GLI repressing GLI(R) states is lost in cancer. Here, the acquisition of GLI(A) levels above a given threshold is predicted to lead to advanced malignant stages. In this review we highlight the concepts of the GLI code, the oncogenic load, the context-dependency of GLI action, and different modes of signaling integration such as that of HH and EGF. Targeting the GLI code directly or indirectly promises therapeutic benefits beyond the direct blockade of individual pathways.
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Affiliation(s)
- Fritz Aberger
- Department of Molecular Biology, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria.
| | - Ariel Ruiz i Altaba
- Department of Genetic Medicine and Development, University of Geneva Medical School, 8242 CMU, 1 rue Michel Servet, CH-1211 Geneva, Switzerland.
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Transcriptional regulation of graded Hedgehog signaling. Semin Cell Dev Biol 2014; 33:73-80. [PMID: 24862856 DOI: 10.1016/j.semcdb.2014.05.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 02/06/2023]
Abstract
The Hedgehog (Hh) pathway plays conserved roles in regulating a diverse spectrum of developmental processes. In some developmental contexts, a gradient of Hh protein specifies multiple cell types in a dose-dependent fashion, thereby acting as a morphogen. Hh signaling ultimately acts on the transcriptional level through GLI proteins. In the presence of Hh signaling full length GLI proteins act as transcriptional activators of target genes. Conversely, in the absence of Hh, GLI proteins act as transcriptional repressors. This review will highlight mechanisms contributing to how graded Hh signaling might translate to differential GLI activity and be interpreted into distinct transcriptional responses.
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