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Lu Y, Berenson A, Lane R, Guelin I, Li Z, Chen Y, Shah S, Yin M, Soto-Ugaldi LF, Fiszbein A, Fuxman Bass JI. A large-scale cancer-specific protein-DNA interaction network. Life Sci Alliance 2024; 7:e202402641. [PMID: 39013578 PMCID: PMC11252446 DOI: 10.26508/lsa.202402641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
Cancer development and progression are generally associated with gene dysregulation, often resulting from changes in the transcription factor (TF) sequence or expression. Identifying key TFs involved in cancer gene regulation provides a framework for potential new therapeutics. This study presents a large-scale cancer gene TF-DNA interaction network, as well as an extensive promoter clone resource for future studies. Highly connected TFs bind to promoters of genes associated with either good or poor cancer prognosis, suggesting that strategies aimed at shifting gene expression balance between these two prognostic groups may be inherently complex. However, we identified potential for oncogene-targeted therapeutics, with half of the tested oncogenes being potentially repressed by influencing specific activators or bifunctional TFs. Finally, we investigate the role of intrinsically disordered regions within the key cancer-related TF ESR1 in DNA binding and transcriptional activity, and found that these regions can have complex trade-offs in TF function. Altogether, our study broadens our knowledge of the TFs involved in cancer gene regulation and provides a valuable resource for future studies and therapeutics.
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Affiliation(s)
- Yunwei Lu
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Anna Berenson
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Ryan Lane
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Isabelle Guelin
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Zhaorong Li
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
| | - Yilin Chen
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Sakshi Shah
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Meimei Yin
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | | | - Ana Fiszbein
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
| | - Juan Ignacio Fuxman Bass
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
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2
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Greenwood M, Gillard BT, Murphy D, Greenwood MP. Dimerization of hub protein DYNLL1 and bZIP transcription factor CREB3L1 enhances transcriptional activation of CREB3L1 target genes like arginine vasopressin. Peptides 2024; 179:171269. [PMID: 38960286 DOI: 10.1016/j.peptides.2024.171269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024]
Abstract
bZIP transcription factors can function as homodimers or heterodimers through interactions with their disordered coiled-coil domain. Such dimer assemblies are known to influence DNA-binding specificity and/or the recruitment of binding partners, which can cause a functional switch of a transcription factor from being an activator to a repressor. We recently identified the genomic targets of a bZIP transcription factor called CREB3L1 in rat hypothalamic supraoptic nucleus by ChIP-seq. The objective of this study was to investigate the CREB3L1 protein-to-protein interactome of which little is known. For this approach, we created and screened a rat supraoptic nucleus yeast two-hybrid prey library with the bZIP region of rat CREB3L1 as the bait. Our yeast two-hybrid approach captured five putative CREB3L1 interacting prey proteins in the supraoptic nucleus. One interactor was selected by bioinformatic analyses for more detailed investigation by co-immunoprecipitation, immunofluorescent cellular localisation, and reporter assays in vitro. Here we identify dimerisation hub protein Dynein Light Chain LC8-Type 1 as a CREB3L1 interacting protein that in vitro enhances CREB3L1 activation of target genes.
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Affiliation(s)
- Mingkwan Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom
| | - Benjamin T Gillard
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom
| | - David Murphy
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom
| | - Michael P Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom.
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3
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Wilson-Verdugo M, Bustos-García B, Adame-Guerrero O, Hersch-González J, Cano-Domínguez N, Soto-Nava M, Acosta CA, Tusie-Luna T, Avila-Rios S, Noriega LG, Valdes VJ. Reversal of high-glucose-induced transcriptional and epigenetic memories through NRF2 pathway activation. Life Sci Alliance 2024; 7:e202302382. [PMID: 38755006 PMCID: PMC11099870 DOI: 10.26508/lsa.202302382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Diabetes complications such as nephropathy, retinopathy, or cardiovascular disease arise from vascular dysfunction. In this context, it has been observed that past hyperglycemic events can induce long-lasting alterations, a phenomenon termed "metabolic memory." In this study, we evaluated the genome-wide gene expression and chromatin accessibility alterations caused by transient high-glucose exposure in human endothelial cells (ECs) in vitro. We found that cells exposed to high glucose exhibited substantial gene expression changes in pathways known to be impaired in diabetes, many of which persist after glucose normalization. Chromatin accessibility analysis also revealed that transient hyperglycemia induces persistent alterations, mainly in non-promoter regions identified as enhancers with neighboring genes showing lasting alterations. Notably, activation of the NRF2 pathway through NRF2 overexpression or supplementation with the plant-derived compound sulforaphane, effectively reverses the glucose-induced transcriptional and chromatin accessibility memories in ECs. These findings underscore the enduring impact of transient hyperglycemia on ECs' transcriptomic and chromatin accessibility profiles, emphasizing the potential utility of pharmacological NRF2 pathway activation in mitigating and reversing the high-glucose-induced transcriptional and epigenetic alterations.
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Affiliation(s)
- Martí Wilson-Verdugo
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Brandon Bustos-García
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Olga Adame-Guerrero
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Jaqueline Hersch-González
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Nallely Cano-Domínguez
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Maribel Soto-Nava
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | | | - Teresa Tusie-Luna
- Unidad de Biología Molecular y Medicina Genómica Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, Ciudad de México, Mexico
| | - Santiago Avila-Rios
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Lilia G Noriega
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Victor J Valdes
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
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4
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Li X, Gong X, Lin H, Rao S, Shen L, Chen C, Wu Z, Li H, Liu Q, Zhong Y. Genome-wide analysis of the bZIP gene family in Cinnamomum camphora ('Gantong 1') reveals the putative function in anthocyanin biosynthesis. Heliyon 2024; 10:e34311. [PMID: 39082037 PMCID: PMC11284375 DOI: 10.1016/j.heliyon.2024.e34311] [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: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
Basic leucine zipper (bZIP) transcription factors (TFs) regulate plant development, growth, and secondary metabolism. The formation of red bark of new ornamental cultivar 'Gantong 1' is regulated mainly by anthocyanin anabolism. However, it is unclear whether and which bZIP TFs are involved in this process. We identified 89 genes encoding CcbZIP TFs in Cinnamomum camphora genome that could be divided into 14 subfamilies with similar gene structures and conserved motifs. CcbZIP38 and CcbZIP57 were highly conserved compared to HY5 in Arabidopsis thaliana and they were highly expressed in the bark and leaves of 'Gantong 1' at different stages. The target gene enrichment analysis showed that indicating indirect involvement of CcbZIP38 and CcbZIP57 in the regulation of anthocyanin synthesis. Our study contributes to understanding the molecular mechanism of anthocyanin synthesis regulation by CcbZIP TFs and provides a theoretical basis for genetic improvement of ornamental traits in C. camphora.
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Affiliation(s)
- Xiuqi Li
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Xue Gong
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Hanbin Lin
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Shupei Rao
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Le Shen
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Caihui Chen
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Zhaoxiang Wu
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Huihu Li
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Qiaoli Liu
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Yongda Zhong
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
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Wang G, Chen B, Zhang X, Du G, Han G, Liu J, Peng Y. The basic leucine zipper domain (bZIP) transcription factor BbYap1 promotes evasion of host humoral immunity and regulates lipid homeostasis contributing to fungal virulence in Beauveria bassiana. mSphere 2024; 9:e0035124. [PMID: 38926907 PMCID: PMC11288043 DOI: 10.1128/msphere.00351-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Basic leucine zipper domain transcription factors (TFs), of which yeast activator protein (Yap) is a significant class, are crucial for the development of sclerotia, the stress response, vegetative growth, and spore adhesion. Nevertheless, nothing is known about how Yap TFs contribute to the pathogenicity of entomopathogenic fungus. In this work, Beauveria bassiana was used to identify and knock out the yeast gene BbYap1, which is similar to Yap. The BbYap1 gene deletion has an impact on lipid homeostasis of B. bassiana; oleic acid, for example, dropped by 95.69%. The BbYap1 mutant exhibited much less virulence and vegetative development in comparison to the wild strain, while demonstrating a greater sensitivity to chemical stress. It is noteworthy that the physiological abnormalities brought on by BbYap1 deletion were largely repaired by the addition of exogenous oleic acid, as seen by the notable increase in insect survival in the blood cavity injection group. Following infection with the BbYap1 mutant, the host exhibits a considerable down-regulation of the expression of β-1,3-glucan recognition protein, gallerimycin, gloverin, and moricin-like protein genes. Likewise, the introduction of exogenous oleic acid markedly increased the host's expression of the aforementioned genes. In summary, BbYap1 regulates cellular enzyme lipid homeostasis and fungal virulence by eluding host humoral defense, which contributes to fungal chemical stress and vegetative development. IMPORTANCE Entomopathogenic fungi (EPF) offer an effective and eco-friendly alternative to curb insect populations in biocontrol strategy. When EPF enter the hemolymph of their host, they encounter a variety of stress reactions, such as immunological and oxidative stress. Basic leucine zipper domain transcription factors, of which yeast activator protein (Yap) is a significant class, have diverse biological functions related to metabolism, development, reproduction, conidiation, stress responses, and pathogenicity. This study demonstrates that BbYap1 of Beauveria bassiana regulates cellular enzyme lipid homeostasis and fungal virulence by eluding host humoral defense, which contributes to fungal chemical stress and vegetative development. These findings offer fresh perspectives for comprehending molecular roles of YAP in EPF.
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Affiliation(s)
- Guang Wang
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Bin Chen
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Xu Zhang
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Guangzu Du
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Guangyu Han
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology, School of Life Science, Yunnan Normal University, Kunming, China
| | - Yuejin Peng
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
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6
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Cho Y. Arabidopsis AGB1 participates in salinity response through bZIP17-mediated unfolded protein response. BMC PLANT BIOLOGY 2024; 24:586. [PMID: 38902609 PMCID: PMC11191249 DOI: 10.1186/s12870-024-05296-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Plant heterotrimeric G proteins respond to various environmental stresses, including high salinity. It is known that Gβ subunit AGB1 functions in maintaining local and systemic Na+/K+ homeostasis to accommodate ionic toxicity under salt stress. However, whether AGB1 contributes to regulating gene expression for seedling's survival under high salinity remains unclear. RESULTS We showed that AGB1-Venus localized to nuclei when facing excessive salt, and the induction of a set of bZIP17-dependent salt stress-responsive genes was reduced in the agb1 mutant. We confirmed both genetic and physical interactions of AGB1 and bZIP17 in plant salinity response by comparing salt responses in the single and double mutants of agb1 and bzip17 and by BiFC assay, respectively. In addition, we show that AGB1 depletion decreases nuclei-localization of transgenic mRFP-bZIP17 under salt stress, as shown in s1p s2p double mutant in the Agrobacteria-mediated transient mRFP-bZIP17 expression in young seedlings. CONCLUSIONS Our results indicate that AGB1 functions in S1P and/or S2P-mediated proteolytic processing of bZIP17 under salt stress to regulate the induction of salinity-responsive gene expression.
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Affiliation(s)
- Yueh Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan.
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7
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Madhuri S, Lepetit B, Fürst AH, Kroth PG. A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components. PLANTS (BASEL, SWITZERLAND) 2024; 13:1465. [PMID: 38891274 PMCID: PMC11174801 DOI: 10.3390/plants13111465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Plants and algae use light not only for driving photosynthesis but also to sense environmental cues and to adjust their circadian clocks via photoreceptors. Aureochromes are blue-light-dependent photoreceptors that also function as transcription factors, possessing both a LOV and a bZIP domain. Aureochromes so far have only been detected in Stramenopile algae, which include the diatoms. Four paralogues of aureochromes have been identified in the pennate model diatom Phaeodactylum tricornutum: PtAureo1a, 1b, 1c, and 2. While it was shown recently that diatoms have a diel rhythm, the molecular mechanisms and components regulating it are still largely unknown. Diel gene expression analyses of wild-type P. tricornutum, a PtAureo1a knockout strain, and the respective PtAureo1 complemented line revealed that all four aureochromes have a different diel regulation and that PtAureo1a has a strong co-regulatory influence on its own transcription, as well as on that of other genes encoding different blue-light photoreceptors (CPF1, 2 and 4), proteins involved in photoprotection (Lhcx1), and specific bHLH transcription factors (RITMO1). Some of these genes completely lost their circadian expression in the PtAureo1a KO mutant. Our results suggest a major involvement of aureochromes in the molecular clock of diatoms.
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Affiliation(s)
| | | | | | - Peter G. Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany; (S.M.); (B.L.); (A.H.F.)
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8
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Ledesma-Dominguez L, Carbajal-Degante E, Moreno-Hagelsieb G, Perez-Rueda E. DeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes. Sci Rep 2024; 14:9155. [PMID: 38644393 DOI: 10.1038/s41598-024-59487-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/11/2024] [Indexed: 04/23/2024] Open
Abstract
Deep learning models (DLMs) have gained importance in predicting, detecting, translating, and classifying a diversity of inputs. In bioinformatics, DLMs have been used to predict protein structures, transcription factor-binding sites, and promoters. In this work, we propose a hybrid model to identify transcription factors (TFs) among prokaryotic and eukaryotic protein sequences, named Deep Regulation (DeepReg) model. Two architectures were used in the DL model: a convolutional neural network (CNN), and a bidirectional long-short-term memory (BiLSTM). DeepReg reached a precision of 0.99, a recall of 0.97, and an F1-score of 0.98. The quality of our predictions, the bias-variance trade-off approach, and the characterization of new TF predictions were evaluated and compared against those produced by DeepTFactor, as well as against experimental data from three model organisms. Predictions based on our DLM tended to exhibit less variance and bias than those from DeepTFactor, thus increasing reliability and decreasing overfitting.
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Affiliation(s)
- Leonardo Ledesma-Dominguez
- Posgrado en Ciencia en Ingeniería de la Computación, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, 04510, Mexico City, México.
| | - Erik Carbajal-Degante
- Coordinación de Universidad Abierta y Educación Digital (CUAED), Universidad Nacional Autónoma de México, 04510, Mexico City, México
| | | | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica del Estado de Yucatán, Universidad Nacional Autónoma de México, Mérida, Yucatán, México.
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9
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Fang Y, Bansal K, Mostafavi S, Benoist C, Mathis D. AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerization. Nature 2024; 628:400-407. [PMID: 38480882 PMCID: PMC11091860 DOI: 10.1038/s41586-024-07169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
AIRE is an unconventional transcription factor that enhances the expression of thousands of genes in medullary thymic epithelial cells and promotes clonal deletion or phenotypic diversion of self-reactive T cells1-4. The biological logic of AIRE's target specificity remains largely unclear as, in contrast to many transcription factors, it does not bind to a particular DNA sequence motif. Here we implemented two orthogonal approaches to investigate AIRE's cis-regulatory mechanisms: construction of a convolutional neural network and leveraging natural genetic variation through analysis of F1 hybrid mice5. Both approaches nominated Z-DNA and NFE2-MAF as putative positive influences on AIRE's target choices. Genome-wide mapping studies revealed that Z-DNA-forming and NFE2L2-binding motifs were positively associated with the inherent ability of a gene's promoter to generate DNA double-stranded breaks, and promoters showing strong double-stranded break generation were more likely to enter a poised state with accessible chromatin and already-assembled transcriptional machinery. Consequently, AIRE preferentially targets genes with poised promoters. We propose a model in which Z-DNA anchors the AIRE-mediated transcriptional program by enhancing double-stranded break generation and promoter poising. Beyond resolving a long-standing mechanistic conundrum, these findings suggest routes for manipulating T cell tolerance.
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Affiliation(s)
- Yuan Fang
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Kushagra Bansal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
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10
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Im SH, Lepetit B, Mosesso N, Shrestha S, Weiss L, Nymark M, Roellig R, Wilhelm C, Isono E, Kroth PG. Identification of promoter targets by Aureochrome 1a in the diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1834-1851. [PMID: 38066674 DOI: 10.1093/jxb/erad478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 12/04/2023] [Indexed: 03/28/2024]
Abstract
Aureochromes (AUREOs) are unique blue light receptors and transcription factors found only in stramenopile algae. While each of the four AUREOs identified in the diatom Phaeodactylum tricornutum may have a specific function, PtAUREO1a has been shown to have a strong impact on overall gene regulation, when light changes from red to blue light conditions. Despite its significance, the molecular mechanism of PtAUREO1a is largely unexplored. To comprehend the overall process of gene regulation by PtAUREO1a, we conducted a series of in vitro and in vivo experiments, including pull-down assays, yeast one-hybrid experiments, and phenotypical characterization using recombinant PtAUREOs and diatom mutant lines expressing a modified PtAureo1a gene. We describe the distinct light absorption properties of four PtAUREOs and the formation of all combinations of their potential dimers. We demonstrate the capability of PtAUREO1a and 1b to activate the genes, diatom-specific cyclin 2, PtAureo1a, and PtAureo1c under both light and dark conditions. Using mutant lines expressing a modified PtAUREO1a protein with a considerably reduced light absorption, we found novel evidence that PtAUREO1a regulates the expression of PtLHCF15, which is essential for red light acclimation. Based on current knowledge, we present a working model of PtAUREO1a gene regulation properties.
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Affiliation(s)
- Soo Hyun Im
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
- Molecular Stress Physiology, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany
| | - Niccolò Mosesso
- Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sandeep Shrestha
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Laura Weiss
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marianne Nymark
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Robert Roellig
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Christian Wilhelm
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Erika Isono
- Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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11
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Corne A, Adolphe F, Estaquier J, Gaumer S, Corsi JM. ATF4 Signaling in HIV-1 Infection: Viral Subversion of a Stress Response Transcription Factor. BIOLOGY 2024; 13:146. [PMID: 38534416 DOI: 10.3390/biology13030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/28/2024]
Abstract
Cellular integrated stress response (ISR), the mitochondrial unfolded protein response (UPRmt), and IFN signaling are associated with viral infections. Activating transcription factor 4 (ATF4) plays a pivotal role in these pathways and controls the expression of many genes involved in redox processes, amino acid metabolism, protein misfolding, autophagy, and apoptosis. The precise role of ATF4 during viral infection is unclear and depends on cell hosts, viral agents, and models. Furthermore, ATF4 signaling can be hijacked by pathogens to favor viral infection and replication. In this review, we summarize the ATF4-mediated signaling pathways in response to viral infections, focusing on human immunodeficiency virus 1 (HIV-1). We examine the consequences of ATF4 activation for HIV-1 replication and reactivation. The role of ATF4 in autophagy and apoptosis is explored as in the context of HIV-1 infection programmed cell deaths contribute to the depletion of CD4 T cells. Furthermore, ATF4 can also participate in the establishment of innate and adaptive immunity that is essential for the host to control viral infections. We finally discuss the putative role of the ATF4 paralogue, named ATF5, in HIV-1 infection. This review underlines the role of ATF4 at the crossroads of multiple processes reflecting host-pathogen interactions.
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Affiliation(s)
- Adrien Corne
- Laboratoire de Génétique et Biologie Cellulaire, Université Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, 78000 Versailles, France
- CHU de Québec Research Center, Laval University, Quebec City, QC G1V 4G2, Canada
| | - Florine Adolphe
- Laboratoire de Génétique et Biologie Cellulaire, Université Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, 78000 Versailles, France
| | - Jérôme Estaquier
- CHU de Québec Research Center, Laval University, Quebec City, QC G1V 4G2, Canada
- INSERM U1124, Université Paris Cité, 75006 Paris, France
| | - Sébastien Gaumer
- Laboratoire de Génétique et Biologie Cellulaire, Université Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, 78000 Versailles, France
| | - Jean-Marc Corsi
- Laboratoire de Génétique et Biologie Cellulaire, Université Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, 78000 Versailles, France
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12
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Bernardini A, Tora L. Co-translational Assembly Pathways of Nuclear Multiprotein Complexes Involved in the Regulation of Gene Transcription. J Mol Biol 2024; 436:168382. [PMID: 38061625 DOI: 10.1016/j.jmb.2023.168382] [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: 10/25/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023]
Abstract
Most factors that regulate gene transcription in eukaryotic cells are multimeric, often large, protein complexes. The understanding of the biogenesis pathways of such large and heterogeneous protein assemblies, as well as the dimerization partner choice among transcription factors, is crucial to interpret and control gene expression programs and consequent cell fate decisions. Co-translational assembly (Co-TA) is thought to play key roles in the biogenesis of protein complexes by directing complex formation during protein synthesis. In this review we discuss the principles of Co-TA with a special focus for the assembly of transcription regulatory complexes. We outline the expected molecular advantages of establishing co-translational interactions, pointing at the available, or missing, evidence for each of them. We hypothesize different molecular mechanisms based on Co-TA to explain the allocation "dilemma" of paralog proteins and subunits shared by different transcription complexes. By taking as a paradigm the different assembly pathways employed by three related transcription regulatory complexes (TFIID, SAGA and ATAC), we discuss alternative Co-TA strategies for nuclear multiprotein complexes and the widespread - yet specific - use of Co-TA for the formation of nuclear complexes involved in gene transcription. Ultimately, we outlined a series of open questions which demand well-defined lines of research to investigate the principles of gene regulation that rely on the coordinated assembly of protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
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13
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Liu Y, Han X, Dai Y, Chen Z. bZIP transcription factor FabR: Redox-dependent mechanism controlling docosahexaenoic acid biosynthesis and H 2O 2 stress response in Schizochytrium sp. Free Radic Biol Med 2024; 210:246-257. [PMID: 38042223 DOI: 10.1016/j.freeradbiomed.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Schizochytrium sp. is an important industrial strain for commercial production of docosahexaenoic acid (DHA), which plays essential physiological roles in infant development and human health. The regulatory network for DHA biosynthesis and lipid accumulation in Schizochytrium remains poorly understood. FabR (fatty acid biosynthesis repressor), a basic leucine zipper (bZIP) transcription factor, was transcriptionally downregulated under low-nitrogen condition. Deletion of fabR gene (mutant ΔfabR) increased production of total lipids and DHA by 30.1% and 46.5%, respectively. ΔfabR displayed H2O2 stress resistance higher than that of parental strain or complementation strain CfabR. FabR bound specifically to 7-bp pseudo-palindromic sequence 5'-ATTSAAT-3' in upstream regions and repressed transcription of fatty acid biosynthesis genes (acl, fas, pfa) and antioxidant defense genes (cat, sod1, sod2, gpx). DNA binding activity of FabR was regulated in a redox-dependent manner. Under oxidative condition, FabR forms intermolecular disulfide bonds between two Cys46 residues of dimers; its DNA binding activity is thereby lost, and the transcription of its target genes is enhanced through derepression. Our findings clarify the redox-dependent mechanism that modulates FabR activity governing lipid and DHA biosynthesis and H2O2 stress response in Schizochytrium.
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Affiliation(s)
- Yana Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiao Han
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yujie Dai
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhi Chen
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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14
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Kalinin A, Zubkova E, Menshikov M. Integrated Stress Response (ISR) Pathway: Unraveling Its Role in Cellular Senescence. Int J Mol Sci 2023; 24:17423. [PMID: 38139251 PMCID: PMC10743681 DOI: 10.3390/ijms242417423] [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: 11/02/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Cellular senescence is a complex process characterized by irreversible cell cycle arrest. Senescent cells accumulate with age, promoting disease development, yet the absence of specific markers hampers the development of selective anti-senescence drugs. The integrated stress response (ISR), an evolutionarily highly conserved signaling network activated in response to stress, globally downregulates protein translation while initiating the translation of specific protein sets including transcription factors. We propose that ISR signaling plays a central role in controlling senescence, given that senescence is considered a form of cellular stress. Exploring the intricate relationship between the ISR pathway and cellular senescence, we emphasize its potential as a regulatory mechanism in senescence and cellular metabolism. The ISR emerges as a master regulator of cellular metabolism during stress, activating autophagy and the mitochondrial unfolded protein response, crucial for maintaining mitochondrial quality and efficiency. Our review comprehensively examines ISR molecular mechanisms, focusing on ATF4-interacting partners, ISR modulators, and their impact on senescence-related conditions. By shedding light on the intricate relationship between ISR and cellular senescence, we aim to inspire future research directions and advance the development of targeted anti-senescence therapies based on ISR modulation.
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Affiliation(s)
- Alexander Kalinin
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia; (A.K.); (E.Z.)
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ekaterina Zubkova
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia; (A.K.); (E.Z.)
| | - Mikhail Menshikov
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia; (A.K.); (E.Z.)
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15
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Parres-Gold J, Levine M, Emert B, Stuart A, Elowitz MB. Principles of Computation by Competitive Protein Dimerization Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564854. [PMID: 37961250 PMCID: PMC10634983 DOI: 10.1101/2023.10.30.564854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Many biological signaling pathways employ proteins that competitively dimerize in diverse combinations. These dimerization networks can perform biochemical computations, in which the concentrations of monomers (inputs) determine the concentrations of dimers (outputs). Despite their prevalence, little is known about the range of input-output computations that dimerization networks can perform (their "expressivity") and how it depends on network size and connectivity. Using a systematic computational approach, we demonstrate that even small dimerization networks (3-6 monomers) are expressive, performing diverse multi-input computations. Further, dimerization networks are versatile, performing different computations when their protein components are expressed at different levels, such as in different cell types. Remarkably, individual networks with random interaction affinities, when large enough (≥8 proteins), can perform nearly all (~90%) potential one-input network computations merely by tuning their monomer expression levels. Thus, even the simple process of competitive dimerization provides a powerful architecture for multi-input, cell-type-specific signal processing.
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Affiliation(s)
- Jacob Parres-Gold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Matthew Levine
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew Stuart
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B. Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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16
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Berenson A, Lane R, Soto-Ugaldi LF, Patel M, Ciausu C, Li Z, Chen Y, Shah S, Santoso C, Liu X, Spirohn K, Hao T, Hill DE, Vidal M, Fuxman Bass JI. Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors. Nat Commun 2023; 14:6570. [PMID: 37853017 PMCID: PMC10584920 DOI: 10.1038/s41467-023-42445-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Cooperativity and antagonism between transcription factors (TFs) can drastically modify their binding to regulatory DNA elements. While mapping these relationships between TFs is important for understanding their context-specific functions, existing approaches either rely on DNA binding motif predictions, interrogate one TF at a time, or study individual TFs in parallel. Here, we introduce paired yeast one-hybrid (pY1H) assays to detect cooperativity and antagonism across hundreds of TF-pairs at DNA regions of interest. We provide evidence that a wide variety of TFs are subject to modulation by other TFs in a DNA region-specific manner. We also demonstrate that TF-TF relationships are often affected by alternative isoform usage and identify cooperativity and antagonism between human TFs and viral proteins from human papillomaviruses, Epstein-Barr virus, and other viruses. Altogether, pY1H assays provide a broadly applicable framework to study how different functional relationships affect protein occupancy at regulatory DNA regions.
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Affiliation(s)
- Anna Berenson
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Mahir Patel
- Department of Computer Science, Boston University, Boston, MA, 02215, USA
| | - Cosmin Ciausu
- Department of Computer Science, Boston University, Boston, MA, 02215, USA
| | - Zhaorong Li
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Yilin Chen
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Sakshi Shah
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Xing Liu
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, 02215, USA.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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17
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Örd T, Örd D, Adler P, Örd T. Genome-wide census of ATF4 binding sites and functional profiling of trait-associated genetic variants overlapping ATF4 binding motifs. PLoS Genet 2023; 19:e1011014. [PMID: 37906604 PMCID: PMC10637723 DOI: 10.1371/journal.pgen.1011014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/10/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023] Open
Abstract
Activating Transcription Factor 4 (ATF4) is an important regulator of gene expression in stress responses and developmental processes in many cell types. Here, we catalogued ATF4 binding sites in the human genome and identified overlaps with trait-associated genetic variants. We probed these genetic variants for allelic regulatory activity using a massively parallel reporter assay (MPRA) in HepG2 hepatoma cells exposed to tunicamycin to induce endoplasmic reticulum stress and ATF4 upregulation. The results revealed that in the majority of cases, the MPRA allelic activity of these SNPs was in agreement with the nucleotide preference seen in the ATF4 binding motif from ChIP-Seq. Luciferase and electrophoretic mobility shift assays in additional cellular models further confirmed ATF4-dependent regulatory effects for the SNPs rs532446 (GADD45A intronic; linked to hematological parameters), rs7011846 (LPL upstream; myocardial infarction), rs2718215 (diastolic blood pressure), rs281758 (psychiatric disorders) and rs6491544 (educational attainment). CRISPR-Cas9 disruption and/or deletion of the regulatory elements harboring rs532446 and rs7011846 led to the downregulation of GADD45A and LPL, respectively. Thus, these SNPs could represent examples of GWAS genetic variants that affect gene expression by altering ATF4-mediated transcriptional activation.
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Affiliation(s)
- Tiit Örd
- Institute of Genomics, University of Tartu, Tartu, Estonia
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Daima Örd
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Priit Adler
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Tõnis Örd
- Institute of Genomics, University of Tartu, Tartu, Estonia
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18
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Liu K, Xiao Y, Gan L, Li W, Zhang J, Min J. Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors. Nucleic Acids Res 2023; 51:8270-8282. [PMID: 37409559 PMCID: PMC10450164 DOI: 10.1093/nar/gkad583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
The TFAP2 family regulates gene expression during differentiation, development, and organogenesis, and includes five homologs in humans. They all possess a highly conserved DNA binding domain (DBD) followed by a helix-span-helix (HSH) domain. The DBD-HSH tandem domain specifically binds to a GCC(N3)GGC consensus sequence, but the precise recognition mechanisms remain unclear. Here, we found that TFAP2 preferred binding to the GCC(N3)GGC sequence, and the pseudo-palindromic GCC and GGC motifs and the length of the central spacer between the two motifs determined their binding specificity. Structural studies revealed that the two flat amphipathic α-helical HSH domains of TFAP2A stacked with each other to form a dimer via hydrophobic interactions, while the stabilized loops from both DBD domains inserted into two neighboring major grooves of the DNA duplex to form base-specific interactions. This specific DNA binding mechanism controlled the length of the central spacer and determined the DNA sequence specificity of TFAP2. Mutations of the TFAP2 proteins are implicated in various diseases. We illustrated that reduction or disruption of the DNA binding ability of the TFAP2 proteins is the primary cause of TFAP2 mutation-associated diseases. Thus, our findings also offer valuable insights into the pathogenesis of disease-associated mutations in TFAP2 proteins.
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Affiliation(s)
- Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yuqing Xiao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Linyao Gan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Weifang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jin Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
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19
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Mukherjee D, Chakraborty S, Bercz L, D’Alesio L, Wedig J, Torok MA, Pfau T, Lathrop H, Jasani S, Guenther A, McGue J, Adu-Ampratwum D, Fuchs JR, Frankel TL, Pietrzak M, Culp S, Strohecker AM, Skardal A, Mace TA. Tomatidine targets ATF4-dependent signaling and induces ferroptosis to limit pancreatic cancer progression. iScience 2023; 26:107408. [PMID: 37554459 PMCID: PMC10405072 DOI: 10.1016/j.isci.2023.107408] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/19/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with high metastasis and therapeutic resistance. Activating transcription factor 4 (ATF4), a master regulator of cellular stress, is exploited by cancer cells to survive. Prior research and data reported provide evidence that high ATF4 expression correlates with worse overall survival in PDAC. Tomatidine, a natural steroidal alkaloid, is associated with inhibition of ATF4 signaling in multiple diseases. Here, we discovered that in vitro and in vivo tomatidine treatment of PDAC cells inhibits tumor growth. Tomatidine inhibited nuclear translocation of ATF4 and reduced the transcriptional binding of ATF4 with downstream promoters. Tomatidine enhanced gemcitabine chemosensitivity in 3D ECM-hydrogels and in vivo. Tomatidine treatment was associated with induction of ferroptosis signaling validated by increased lipid peroxidation, mitochondrial biogenesis, and decreased GPX4 expression in PDAC cells. This study highlights a possible therapeutic approach utilizing a plant-derived metabolite, tomatidine, to target ATF4 activity in PDAC.
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Affiliation(s)
- Debasmita Mukherjee
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Srija Chakraborty
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Lena Bercz
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Liliana D’Alesio
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jessica Wedig
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Molly A. Torok
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Timothy Pfau
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Hannah Lathrop
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shrina Jasani
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Abigail Guenther
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jake McGue
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Adu-Ampratwum
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH 43210, USA
| | - James R. Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH 43210, USA
| | | | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Stacey Culp
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Anne M. Strohecker
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Cancer Biology & Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Aleksander Skardal
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Thomas A. Mace
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Internal Medicine, Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University, Columbus, OH 43210, USA
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20
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Cain B, Webb J, Yuan Z, Cheung D, Lim HW, Kovall R, Weirauch MT, Gebelein B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Res 2023; 51:6055-6072. [PMID: 37114997 PMCID: PMC10325903 DOI: 10.1093/nar/gkad318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023] Open
Abstract
Homeodomain proteins constitute one of the largest families of metazoan transcription factors. Genetic studies have demonstrated that homeodomain proteins regulate many developmental processes. Yet, biochemical data reveal that most bind highly similar DNA sequences. Defining how homeodomain proteins achieve DNA binding specificity has therefore been a long-standing goal. Here, we developed a novel computational approach to predict cooperative dimeric binding of homeodomain proteins using High-Throughput (HT) SELEX data. Importantly, we found that 15 of 88 homeodomain factors form cooperative homodimer complexes on DNA sites with precise spacing requirements. Approximately one third of the paired-like homeodomain proteins cooperatively bind palindromic sequences spaced 3 bp apart, whereas other homeodomain proteins cooperatively bind sites with distinct orientation and spacing requirements. Combining structural models of a paired-like factor with our cooperativity predictions identified key amino acid differences that help differentiate between cooperative and non-cooperative factors. Finally, we confirmed predicted cooperative dimer sites in vivo using available genomic data for a subset of factors. These findings demonstrate how HT-SELEX data can be computationally mined to predict cooperativity. In addition, the binding site spacing requirements of select homeodomain proteins provide a mechanism by which seemingly similar AT-rich DNA sequences can preferentially recruit specific homeodomain factors.
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Affiliation(s)
- Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Jordan Webb
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David Cheung
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Divisions of Human Genetics, Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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21
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Klumpe HE, Garcia-Ojalvo J, Elowitz MB, Antebi YE. The computational capabilities of many-to-many protein interaction networks. Cell Syst 2023; 14:430-446. [PMID: 37348461 PMCID: PMC10318606 DOI: 10.1016/j.cels.2023.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Many biological circuits comprise sets of protein variants that interact with one another in a many-to-many, or promiscuous, fashion. These architectures can provide powerful computational capabilities that are especially critical in multicellular organisms. Understanding the principles of biochemical computations in these circuits could allow more precise control of cellular behaviors. However, these systems are inherently difficult to analyze, due to their large number of interacting molecular components, partial redundancies, and cell context dependence. Here, we discuss recent experimental and theoretical advances that are beginning to reveal how promiscuous circuits compute, what roles those computations play in natural biological contexts, and how promiscuous architectures can be applied for the design of synthetic multicellular behaviors.
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Affiliation(s)
- Heidi E Klumpe
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Yaron E Antebi
- Department of Molecular Genetics, Weizmann Institute of Science 76100, Rehovot, Israel.
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22
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Flanigan KM, Waldrop MA, Martin PT, Alles R, Dunn DM, Alfano LN, Simmons TR, Moore-Clingenpeel M, Burian J, Seok SC, Weiss RB, Vieland VJ. A genome-wide association analysis of loss of ambulation in dystrophinopathy patients suggests multiple candidate modifiers of disease severity. Eur J Hum Genet 2023; 31:663-673. [PMID: 36935420 PMCID: PMC10250491 DOI: 10.1038/s41431-023-01329-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/27/2023] [Accepted: 02/21/2023] [Indexed: 03/21/2023] Open
Abstract
The major determinant of disease severity in Duchenne muscular dystrophy (DMD) or milder Becker muscular dystrophy (BMD) is whether the dystrophin gene (DMD) mutation truncates the mRNA reading frame or allows expression of a partially functional protein. However, even in the complete absence of dystrophin, variability in disease severity is observed, and candidate gene studies have implicated several genes as modifiers. Here we present the largest genome-wide search to date for loci influencing severity in N = 419 DMD patients. Availability of subjects for such studies is quite limited, leading to modest sample sizes, which present a challenge for GWAS design. We have therefore taken special steps to minimize heterogeneity within our dataset at the DMD locus itself, taking a novel approach to mutation classification to effectively exclude the possibility of residual dystrophin expression, and utilized statistical methods that are well adapted to smaller sample sizes, including the use of a novel linear regression-like residual for time to ambulatory loss and the application of evidential statistics for the GWAS approach. Finally, we applied an unbiased in silico pipeline, utilizing functional genomic datasets to explore the potential impact of the best supported SNPs. In all, we obtained eight SNPs (out of 1,385,356 total) with posterior probability of trait-marker association (PPLD) ≥ 0.4, representing six distinct loci. Our analysis prioritized likely non-coding SNP regulatory effects on six genes (ETAA1, PARD6G, GALNTL6, MAN1A1, ADAMTS19, and NCALD), each with plausibility as a DMD modifier. These results support both recurrent and potentially new pathways for intervention in the dystrophinopathies.
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Affiliation(s)
- Kevin M Flanigan
- The Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
- The Departments of Pediatrics, The Ohio State University, Columbus, OH, USA.
- The Departments of Neurology, The Ohio State University, Columbus, OH, USA.
| | - Megan A Waldrop
- The Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- The Departments of Pediatrics, The Ohio State University, Columbus, OH, USA
- The Departments of Neurology, The Ohio State University, Columbus, OH, USA
| | - Paul T Martin
- The Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- The Departments of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Roxane Alles
- The Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Diane M Dunn
- The Department of Human Genetics, University of Utah, Salt Lake, UT, USA
| | - Lindsay N Alfano
- The Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- The Departments of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Tabatha R Simmons
- The Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Melissa Moore-Clingenpeel
- The Battelle Center for Mathematical Medicine, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- The Departments of Statistics, The Ohio State University, Columbus, OH, USA
| | - John Burian
- The Battelle Center for Mathematical Medicine, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Sang-Cheol Seok
- The Battelle Center for Mathematical Medicine, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Robert B Weiss
- The Department of Human Genetics, University of Utah, Salt Lake, UT, USA
| | - Veronica J Vieland
- The Departments of Pediatrics, The Ohio State University, Columbus, OH, USA
- The Battelle Center for Mathematical Medicine, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- The Departments of Statistics, The Ohio State University, Columbus, OH, USA
- Mathematical Medicine, LLC, Chicago, IL, USA
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23
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Li M, Yao T, Lin W, Hinckley WE, Galli M, Muchero W, Gallavotti A, Chen JG, Huang SSC. Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors. Nat Commun 2023; 14:2600. [PMID: 37147307 PMCID: PMC10163045 DOI: 10.1038/s41467-023-38096-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/15/2023] [Indexed: 05/07/2023] Open
Abstract
Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.
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Affiliation(s)
- Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wanru Lin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Will E Hinckley
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
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24
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Alonso CAI, David CD, Toufaily C, Wang Y, Zhou X, Ongaro L, Nudelman G, Nair VD, Ruf-Zamojski F, Boehm U, Sealfon SC, Bernard DJ. Activating Transcription Factor 3 Stimulates Follicle-Stimulating Hormone-β Expression In Vitro But Is Dispensable for Follicle-Stimulating Hormone Production in Murine Gonadotropes In Vivo. Endocrinology 2023; 164:bqad050. [PMID: 36951304 PMCID: PMC10282924 DOI: 10.1210/endocr/bqad050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 03/24/2023]
Abstract
Follicle-stimulating hormone (FSH), a dimeric glycoprotein produced by pituitary gonadotrope cells, regulates spermatogenesis in males and ovarian follicle growth in females. Hypothalamic gonadotropin-releasing hormone (GnRH) stimulates FSHβ subunit gene (Fshb) transcription, though the underlying mechanisms are poorly understood. To address this gap in knowledge, we examined changes in pituitary gene expression in GnRH-deficient mice (hpg) treated with a regimen of exogenous GnRH that increases pituitary Fshb but not luteinizing hormone β (Lhb) messenger RNA levels. Activating transcription factor 3 (Atf3) was among the most upregulated genes. Activating transcription factor 3 (ATF3) can heterodimerize with members of the activator protein 1 family to regulate gene transcription. Co-expression of ATF3 with JunB stimulated murine Fshb, but not Lhb, promoter-reporter activity in homologous LβT2b cells. ATF3 also synergized with a constitutively active activin type I receptor to increase endogenous Fshb expression in these cells. Nevertheless, FSH production was intact in gonadotrope-specific Atf3 knockout [conditional knockout (cKO)] mice. Ovarian follicle development, ovulation, and litter sizes were equivalent between cKOs and controls. Testis weights and sperm counts did not differ between genotypes. Following gonadectomy, increases in LH secretion were enhanced in cKO animals. Though FSH levels did not differ between genotypes, post-gonadectomy increases in pituitary Fshb and gonadotropin α subunit expression were more pronounced in cKO than control mice. These data indicate that ATF3 can selectively stimulate Fshb expression in vitro but is not required for FSH production in vivo.
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Affiliation(s)
- Carlos A I Alonso
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Caroline D David
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Chirine Toufaily
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Ying Wang
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Xiang Zhou
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Luisina Ongaro
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - German Nudelman
- Department of Neurology, Center for Advanced Research on Diagnostic Assay, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assay, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assay, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ulrich Boehm
- Department of Experimental Pharmacology, Center for Molecular Signaling, Saarland University School of Medicine, Homburg 66421, Germany
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assay, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
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25
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Gouveia Roque C, Chung KM, McCurdy EP, Jagannathan R, Randolph LK, Herline-Killian K, Baleriola J, Hengst U. CREB3L2-ATF4 heterodimerization defines a transcriptional hub of Alzheimer's disease gene expression linked to neuropathology. SCIENCE ADVANCES 2023; 9:eadd2671. [PMID: 36867706 PMCID: PMC9984184 DOI: 10.1126/sciadv.add2671] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Gene expression is changed by disease, but how these molecular responses arise and contribute to pathophysiology remains less understood. We discover that β-amyloid, a trigger of Alzheimer's disease (AD), promotes the formation of pathological CREB3L2-ATF4 transcription factor heterodimers in neurons. Through a multilevel approach based on AD datasets and a novel chemogenetic method that resolves the genomic binding profile of dimeric transcription factors (ChIPmera), we find that CREB3L2-ATF4 activates a transcription network that interacts with roughly half of the genes differentially expressed in AD, including subsets associated with β-amyloid and tau neuropathologies. CREB3L2-ATF4 activation drives tau hyperphosphorylation and secretion in neurons, in addition to misregulating the retromer, an endosomal complex linked to AD pathogenesis. We further provide evidence for increased heterodimer signaling in AD brain and identify dovitinib as a candidate molecule for normalizing β-amyloid-mediated transcriptional responses. The findings overall reveal differential transcription factor dimerization as a mechanism linking disease stimuli to the development of pathogenic cellular states.
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Affiliation(s)
- Cláudio Gouveia Roque
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Kyung Min Chung
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Ethan P. McCurdy
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Radhika Jagannathan
- Division of Aging and Dementia, Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lisa K. Randolph
- Doctoral Program in Neurobiology and Behavior, Columbia University, New York, NY, USA
| | - Krystal Herline-Killian
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jimena Baleriola
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain
- Department of Cell Biology and Histology, University of the Basque Country, Leioa, Spain
| | - Ulrich Hengst
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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26
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Peña-Martínez EG, Rivera-Madera A, Pomales-Matos DA, Sanabria-Alberto L, Rosario-Cañuelas BM, Rodríguez-Ríos JM, Carrasquillo-Dones EA, Rodríguez-Martínez JA. Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194906. [PMID: 36690178 PMCID: PMC10013089 DOI: 10.1016/j.bbagrm.2023.194906] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/22/2023]
Abstract
Genome-wide association studies (GWAS) have mapped over 90 % of disease- or trait-associated variants within the non-coding genome, like cis-regulatory elements (CREs). Non-coding single nucleotide polymorphisms (SNPs) are genomic variants that can change how DNA-binding regulatory proteins, like transcription factors (TFs), interact with the genome and regulate gene expression. NKX2-5 is a TF essential for proper heart development, and mutations affecting its function have been associated with congenital heart diseases (CHDs). However, establishing a causal mechanism between non-coding genomic variants and human disease remains challenging. To address this challenge, we identified 8475 SNPs predicted to alter NKX2-5 DNA-binding using a position weight matrix (PWM)-based predictive model. Five variants were prioritized for in vitro validation; four of them are associated with traits and diseases that impact cardiovascular health. The impact of these variants on NKX2-5 binding was evaluated with electrophoretic mobility shift assay (EMSA) using purified recombinant NKX2-5 homeodomain. Binding curves were constructed to determine changes in binding between variant and reference alleles. Variants rs7350789, rs7719885, rs747334, and rs3892630 increased binding affinity, whereas rs61216514 decreased binding by NKX2-5 when compared to the reference genome. Our findings suggest that differential TF-DNA binding affinity can be key in establishing a causal mechanism of pathogenic variants.
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27
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Roura AJ, Szadkowska P, Poleszak K, Dabrowski MJ, Ellert-Miklaszewska A, Wojnicki K, Ciechomska IA, Stepniak K, Kaminska B, Wojtas B. Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications. Clin Epigenetics 2023; 15:29. [PMID: 36850002 PMCID: PMC9972689 DOI: 10.1186/s13148-023-01446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM, WHO grade IV) is an aggressive, primary brain tumor. Despite extensive tumor resection followed by radio- and chemotherapy, life expectancy of GBM patients did not improve over decades. Several studies reported transcription deregulation in GBMs, but regulatory mechanisms driving overexpression of GBM-specific genes remain largely unknown. Transcription in open chromatin regions is directed by transcription factors (TFs) that bind to specific motifs, recruit co-activators/repressors and the transcriptional machinery. Identification of GBM-related TFs-gene regulatory networks may reveal new and targetable mechanisms of gliomagenesis. RESULTS We predicted TFs-regulated networks in GBMs in silico and intersected them with putative TF binding sites identified in the accessible chromatin in human glioma cells and GBM patient samples. The Cancer Genome Atlas and Glioma Atlas datasets (DNA methylation, H3K27 acetylation, transcriptomic profiles) were explored to elucidate TFs-gene regulatory networks and effects of the epigenetic background. In contrast to the majority of tumors, c-Jun expression was higher in GBMs than in normal brain and c-Jun binding sites were found in multiple genes overexpressed in GBMs, including VIM, FOSL2 or UPP1. Binding of c-Jun to the VIM gene promoter was stronger in GBM-derived cells than in cells derived from benign glioma as evidenced by gel shift and supershift assays. Regulatory regions of the majority of c-Jun targets have distinct DNA methylation patterns in GBMs as compared to benign gliomas, suggesting the contribution of DNA methylation to the c-Jun-dependent gene expression. CONCLUSIONS GBM-specific TFs-gene networks identified in GBMs differ from regulatory pathways attributed to benign brain tumors and imply a decisive role of c-Jun in controlling genes that drive glioma growth and invasion as well as a modulatory role of DNA methylation.
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Affiliation(s)
- Adria-Jaume Roura
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Paulina Szadkowska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
- grid.13339.3b0000000113287408Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Katarzyna Poleszak
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Michal J. Dabrowski
- grid.425308.80000 0001 2158 4832Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Ellert-Miklaszewska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Kamil Wojnicki
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Iwona A. Ciechomska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Karolina Stepniak
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bozena Kaminska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartosz Wojtas
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
- grid.419305.a0000 0001 1943 2944Laboratory of Sequencing, Nencki Institute of Experimental Biology, ul. Ludwika Pasteura 3, 02-093 Warsaw, Poland
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28
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Neill G, Masson GR. A stay of execution: ATF4 regulation and potential outcomes for the integrated stress response. Front Mol Neurosci 2023; 16:1112253. [PMID: 36825279 PMCID: PMC9941348 DOI: 10.3389/fnmol.2023.1112253] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
ATF4 is a cellular stress induced bZIP transcription factor that is a hallmark effector of the integrated stress response. The integrated stress response is triggered by phosphorylation of the alpha subunit of the eukaryotic initiation factor 2 complex that can be carried out by the cellular stress responsive kinases; GCN2, PERK, PKR, and HRI. eIF2α phosphorylation downregulates mRNA translation initiation en masse, however ATF4 translation is upregulated. The integrated stress response can output two contradicting outcomes in cells; pro-survival or apoptosis. The mechanism for choice between these outcomes is unknown, however combinations of ATF4 heterodimerisation partners and post-translational modifications have been linked to this regulation. This semi-systematic review article covers ATF4 target genes, heterodimerisation partners and post-translational modifications. Together, this review aims to be a useful resource to elucidate the mechanisms controlling the effects of the integrated stress response. Additional putative roles of the ATF4 protein in cell division and synaptic plasticity are outlined.
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Affiliation(s)
- Graham Neill
- Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
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29
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Pérez-Rodríguez D, Penedo MA, Rivera-Baltanás T, Peña-Centeno T, Burkhardt S, Fischer A, Prieto-González JM, Olivares JM, López-Fernández H, Agís-Balboa RC. MiRNA Differences Related to Treatment-Resistant Schizophrenia. Int J Mol Sci 2023; 24:ijms24031891. [PMID: 36768211 PMCID: PMC9916039 DOI: 10.3390/ijms24031891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/21/2023] Open
Abstract
Schizophrenia (SZ) is a serious mental disorder that is typically treated with antipsychotic medication. Treatment-resistant schizophrenia (TRS) is the condition where symptoms remain after pharmacological intervention, resulting in long-lasting functional and social impairments. As the identification and treatment of a TRS patient requires previous failed treatments, early mechanisms of detection are needed in order to quicken the access to effective therapy, as well as improve treatment adherence. In this study, we aim to find a microRNA (miRNA) signature for TRS, as well as to shed some light on the molecular pathways potentially involved in this severe condition. To do this, we compared the blood miRNAs of schizophrenia patients that respond to medication and TRS patients, thus obtaining a 16-miRNA TRS profile. Then, we assessed the ability of this signature to separate responders and TRS patients using hierarchical clustering, observing that most of them are grouped correctly (~70% accuracy). We also conducted a network, pathway analysis, and bibliography search to spot molecular pathways potentially altered in TRS. We found that the response to stress seems to be a key factor in TRS and that proteins p53, SIRT1, MDM2, and TRIM28 could be the potential mediators of such responses. Finally, we suggest a molecular pathway potentially regulated by the miRNAs of the TRS profile.
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Affiliation(s)
- Daniel Pérez-Rodríguez
- NeuroEpigenetics Lab, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
| | - Maria Aránzazu Penedo
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
- Grupo de Neurofarmacología de Las Adicciones y Los Trastornos Degenerativos (NEUROFAN), Universidad CEU San Pablo, 28925 Madrid, Spain
| | - Tania Rivera-Baltanás
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
| | - Tonatiuh Peña-Centeno
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, 37075 Göttingen, Germany
| | - Susanne Burkhardt
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, 37075 Göttingen, Germany
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, 37075 Göttingen, Germany
| | - José M. Prieto-González
- NeuroEpigenetics Lab, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Servicio de Neurología, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Grupo Trastornos del Movimiento, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
| | - José Manuel Olivares
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
- Department of Psychiatry, Área Sanitaria de Vigo, 36312 Vigo, Spain
| | - Hugo López-Fernández
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
- CINBIO, Department of Computer Science, ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain
- Correspondence: (H.L.-F.); (R.C.A.-B.)
| | - Roberto Carlos Agís-Balboa
- NeuroEpigenetics Lab, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
- Servicio de Neurología, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Grupo Trastornos del Movimiento, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Correspondence: (H.L.-F.); (R.C.A.-B.)
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Hartl L, Roelofs JJTH, Dijk F, Bijlsma MF, Duitman J, Spek CA. C/EBP-Family Redundancy Determines Patient Survival and Lymph Node Involvement in PDAC. Int J Mol Sci 2023; 24:ijms24021537. [PMID: 36675048 PMCID: PMC9867044 DOI: 10.3390/ijms24021537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a dismal disease with a poor clinical prognosis and unsatisfactory treatment options. We previously found that the transcription factor CCAAT/Enhancer-Binding Protein Delta (C/EBPδ) is lowly expressed in PDAC compared to healthy pancreas duct cells, and that patient survival and lymph node involvement in PDAC is correlated with the expression of C/EBPδ in primary tumor cells. C/EBPδ shares a homologous DNA-binding sequence with other C/EBP-proteins, leading to the presumption that other C/EBP-family members might act redundantly and compensate for the loss of C/EBPδ. This implies that patient stratification could be improved when expression levels of multiple C/EBP-family members are considered simultaneously. In this study, we assessed whether the quantification of C/EBPβ or C/EBPγ in addition to that of C/EBPδ might improve the prediction of patient survival and lymph node involvement using a cohort of 68 resectable PDAC patients. Using Kaplan-Meier analyses of patient groups with different C/EBP-expression levels, we found that both C/EBPβ and C/EBPγ can partially compensate for low C/EBPδ and improve patient survival. Further, we uncovered C/EBPβ as a novel predictor of a decreased likelihood of lymph node involvement in PDAC, and found that C/EBPβ and C/EBPδ can compensate for the lack of each other in order to reduce the risk of lymph node involvement. C/EBPγ, on the other hand, appears to promote lymph node involvement in the absence of C/EBPδ. Altogether, our results show that the redundancy of C/EBP-family members might have a profound influence on clinical prognoses and that the expression of both C/EPBβ and C/EBPγ should be taken into account when dichotomizing patients according to C/EBPδ expression.
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Affiliation(s)
- Leonie Hartl
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, 1081 HV Amsterdam, The Netherlands
| | - Joris J. T. H. Roelofs
- Department of Pathology, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Frederike Dijk
- Cancer Center Amsterdam, Cancer Biology and Immunology, 1081 HV Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Maarten F. Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, 1081 HV Amsterdam, The Netherlands
| | - JanWillem Duitman
- Department of Pulmonary Medicine, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Infection & Immunity, Inflammatory Diseases, 1105 AZ Amsterdam, The Netherlands
| | - C. Arnold Spek
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, 1081 HV Amsterdam, The Netherlands
- Correspondence:
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31
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Holland SD, Ramer MS. Microglial activating transcription factor 3 upregulation: An indirect target to attenuate inflammation in the nervous system. Front Mol Neurosci 2023; 16:1150296. [PMID: 37033378 PMCID: PMC10076742 DOI: 10.3389/fnmol.2023.1150296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Activating Transcription Factor 3 (ATF3) is upregulated in reaction to several cellular stressors found in a wide range of pathological conditions to coordinate a transcriptional response. ATF3 was first implicated in the transcriptional reaction to axotomy when its massive upregulation was measured in sensory and motor neuron cell bodies following peripheral nerve injury. It has since been shown to be critical for successful axon regeneration in the peripheral nervous system and a promising target to mitigate regenerative failure in the central nervous system. However, much of the research to date has focused on ATF3's function in neurons, leaving the expression, function, and therapeutic potential of ATF3 in glia largely unexplored. In the immunology literature ATF3 is seen as a master regulator of the innate immune system. Specifically, in macrophages following pathogen or damage associated molecular pattern receptor activation and subsequent cytokine release, ATF3 upregulation abrogates the inflammatory response. Importantly, ATF3 upregulation is not exclusively due to cellular stress exposure but has been achieved by the administration of several small molecules. In the central nervous system, microglia represent the resident macrophage population and are therefore of immediate interest with respect to ATF3 induction. It is our perspective that the potential of inducing ATF3 expression to dampen inflammatory microglial phenotype represents an unexplored therapeutic target and may have synergistic benefits when paired with concomitant neuronal ATF3 upregulation. This would be of particular benefit in pathologies that involve both detrimental inflammation and neuronal damage including spinal cord injury, multiple sclerosis, and stroke.
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32
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Sengoku T, Shiina M, Suzuki K, Hamada K, Sato K, Uchiyama A, Kobayashi S, Oguni A, Itaya H, Kasahara K, Moriwaki H, Watanabe C, Honma T, Okada C, Baba S, Ohta T, Motohashi H, Yamamoto M, Ogata K. Structural basis of transcription regulation by CNC family transcription factor, Nrf2. Nucleic Acids Res 2022; 50:12543-12557. [PMID: 36454022 PMCID: PMC9756947 DOI: 10.1093/nar/gkac1102] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/22/2022] [Accepted: 11/02/2022] [Indexed: 12/05/2022] Open
Abstract
Several basic leucine zipper (bZIP) transcription factors have accessory motifs in their DNA-binding domains, such as the CNC motif of CNC family or the EHR motif of small Maf (sMaf) proteins. CNC family proteins heterodimerize with sMaf proteins to recognize CNC-sMaf binding DNA elements (CsMBEs) in competition with sMaf homodimers, but the functional role of the CNC motif remains elusive. In this study, we report the crystal structures of Nrf2/NFE2L2, a CNC family protein regulating anti-stress transcriptional responses, in a complex with MafG and CsMBE. The CNC motif restricts the conformations of crucial Arg residues in the basic region, which form extensive contact with the DNA backbone phosphates. Accordingly, the Nrf2-MafG heterodimer has approximately a 200-fold stronger affinity for CsMBE than canonical bZIP proteins, such as AP-1 proteins. The high DNA affinity of the CNC-sMaf heterodimer may allow it to compete with the sMaf homodimer on target genes without being perturbed by other low-affinity bZIP proteins with similar sequence specificity.
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Affiliation(s)
- Toru Sengoku
- To whom correspondence should be addressed. Tel: +81 45 787 2590; Fax: +81 45 784 4530;
| | | | - Kae Suzuki
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Ko Sato
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Akiko Uchiyama
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shunsuke Kobayashi
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Asako Oguni
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hayato Itaya
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Hirotomo Moriwaki
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan,JST PRESTO, Yokohama 230-0045, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Chikako Okada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shiho Baba
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Tsutomu Ohta
- Department of Physical Therapy, Faculty of Health and Medical Sciences, Tokoha University, Hamamatsu 431-2102, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8575, Japan
| | - Kazuhiro Ogata
- Correspondence may also be addressed to Kazuhiro Ogata. Tel: +81 45 787 2590; Fax: +81 45 784 4530;
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33
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Assunção AGL. The F-bZIP-regulated Zn deficiency response in land plants. PLANTA 2022; 256:108. [PMID: 36348172 PMCID: PMC9643250 DOI: 10.1007/s00425-022-04019-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
This review describes zinc sensing and transcriptional regulation of the zinc deficiency response in Arabidopsis, and discusses how their evolutionary conservation in land plants facilitates translational approaches for improving the Zn nutritional value of crop species. Zinc is an essential micronutrient for all living organisms due to its presence in a large number of proteins, as a structural or catalytic cofactor. In plants, zinc homeostasis mechanisms comprise uptake from soil, transport and distribution throughout the plant to provide adequate cellular zinc availability. Here, I discuss the transcriptional regulation of the response to zinc deficiency and the zinc sensing mechanisms in Arabidopsis, and their evolutionary conservation in land plants. The Arabidopsis F-group basic region leucine-zipper (F-bZIP) transcription factors bZIP19 and bZIP23 function simultaneously as sensors of intracellular zinc status, by direct binding of zinc ions, and as the central regulators of the zinc deficiency response, with their target genes including zinc transporters from the ZRT/IRT-like Protein (ZIP) family and nicotianamine synthase enzymes that produce the zinc ligand nicotianamine. I note that this relatively simple mechanism of zinc sensing and regulation, together with the evolutionary conservation of F-bZIP transcription factors across land plants, offer important research opportunities. One of them is to use the F-bZIP-regulated zinc deficiency response as a tractable module for evolutionary and comparative functional studies. Another research opportunity is translational research in crop plants, modulating F-bZIP activity as a molecular switch to enhance zinc accumulation. This should become a useful plant-based solution to alleviate effects of zinc deficiency in soils, which impact crop production and crop zinc content, with consequences for human nutrition globally.
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Affiliation(s)
- Ana G L Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark.
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal.
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Wang B, Li L, Liu M, Peng D, Wei A, Hou B, Lei Y, Li X. TaFDL2-1A confers drought stress tolerance by promoting ABA biosynthesis, ABA responses, and ROS scavenging in transgenic wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:722-737. [PMID: 36097863 DOI: 10.1111/tpj.15975] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Plants have developed various protective mechanisms to survive drought stress. Previously, it was shown that a wheat bZIP transcription factor gene TaFD-Like2-1A (TaFDL2-1A) can confer drought tolerance in Arabidopsis. However, the biological functions related to drought stress tolerance of TaFDL2-1A in wheat (Triticum aestivum L.) remain unclear. In the present study, overexpression of TaFDL2-1A in the wheat cultivar Fielder improved drought resistance and conferred abscisic acid (ABA) hypersensitivity. Further analysis showed that overexpression of TaFDL2-1A increased the hypersensitivity of stomata to drought stress and endogenous ABA content under drought conditions. Genetic analysis and transcriptional regulation analysis indicated that TaFDL2-1A binds directly to the promoter fragments of TaRAB21s and TaNCED2s via ACGT core cis-elements, thereby activating their expression, leading to enhanced ABA responses and endogenous ABA accumulation. In addition, our results demonstrate that overexpression of TaFDL2-1A results in higher SOD and GPX activities in wheat under drought conditions by promoting the expression of TaSOD1 and TaGPx1-D, indicating enhanced reactive oxygen species (ROS) scavenging. These results imply that TaFDL2-1A positively regulates ABA biosynthesis, ABA responses, and ROS scavenging to improve drought stress tolerance in transgenic wheat. Our findings improve our understanding of the mechanisms that allow the wheat bZIP transcription factor to improve drought resistance and provide a useful reference gene for breeding programs to enhance drought resistance.
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Affiliation(s)
- Bingxin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liqun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingliu Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - De Peng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Aosong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Beiyuan Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanhong Lei
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
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35
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Yadav Y, Subbaroyan A, Martin OC, Samal A. Relative importance of composition structures and biologically meaningful logics in bipartite Boolean models of gene regulation. Sci Rep 2022; 12:18156. [PMID: 36307465 PMCID: PMC9616893 DOI: 10.1038/s41598-022-22654-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/18/2022] [Indexed: 12/31/2022] Open
Abstract
Boolean networks have been widely used to model gene networks. However, such models are coarse-grained to an extent that they abstract away molecular specificities of gene regulation. Alternatively, bipartite Boolean network models of gene regulation explicitly distinguish genes from transcription factors (TFs). In such bipartite models, multiple TFs may simultaneously contribute to gene regulation by forming heteromeric complexes, thus giving rise to composition structures. Since bipartite Boolean models are relatively recent, an empirical investigation of their biological plausibility is lacking. Here, we estimate the prevalence of composition structures arising through heteromeric complexes. Moreover, we present an additional mechanism where composition structures may arise as a result of multiple TFs binding to cis-regulatory regions and provide empirical support for this mechanism. Next, we compare the restriction in BFs imposed by composition structures and by biologically meaningful properties. We find that though composition structures can severely restrict the number of Boolean functions (BFs) driving a gene, the two types of minimally complex BFs, namely nested canalyzing functions (NCFs) and read-once functions (RoFs), are comparatively more restrictive. Finally, we find that composition structures are highly enriched in real networks, but this enrichment most likely comes from NCFs and RoFs.
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Affiliation(s)
- Yasharth Yadav
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
| | - Ajay Subbaroyan
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | - Olivier C Martin
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France.
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France.
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India.
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India.
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36
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Antony C, George SS, Blum J, Somers P, Thorsheim CL, Wu-Corts DJ, Ai Y, Gao L, Lv K, Tremblay MG, Moss T, Tan K, Wilusz JE, Ganley ARD, Pimkin M, Paralkar VR. Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell 2022; 82:3826-3839.e9. [PMID: 36113481 PMCID: PMC9588704 DOI: 10.1016/j.molcel.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/23/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
Ribosomal RNAs (rRNAs) are the most abundant cellular RNAs, and their synthesis from rDNA repeats by RNA polymerase I accounts for the bulk of all transcription. Despite substantial variation in rRNA transcription rates across cell types, little is known about cell-type-specific factors that bind rDNA and regulate rRNA transcription to meet tissue-specific needs. Using hematopoiesis as a model system, we mapped about 2,200 ChIP-seq datasets for 250 transcription factors (TFs) and chromatin proteins to human and mouse rDNA and identified robust binding of multiple TF families to canonical TF motifs on rDNA. Using a 47S-FISH-Flow assay developed for nascent rRNA quantification, we demonstrated that targeted degradation of C/EBP alpha (CEBPA), a critical hematopoietic TF with conserved rDNA binding, caused rapid reduction in rRNA transcription due to reduced RNA Pol I occupancy. Our work identifies numerous potential rRNA regulators and provides a template for dissection of TF roles in rRNA transcription.
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Affiliation(s)
- Charles Antony
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Subin S George
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Justin Blum
- The College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patrick Somers
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chelsea L Thorsheim
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dexter J Wu-Corts
- The College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuxi Ai
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Long Gao
- Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Kaosheng Lv
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Michel G Tremblay
- Laboratory of Growth and Development, St Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre (CRCHU de Québec-Université Laval), Québec, QC G1R 3S3, Canada
| | - Tom Moss
- Laboratory of Growth and Development, St Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre (CRCHU de Québec-Université Laval), Québec, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec, QC G1V 0A6, Canada
| | - Kai Tan
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland 0623, New Zealand; Digital Life Institute, University of Auckland, Auckland 0632, New Zealand
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Vikram R Paralkar
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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37
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Ghoshdastidar D, Bansal M. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif. Biophys J 2022; 121:3987-4000. [PMID: 35978548 PMCID: PMC9674967 DOI: 10.1016/j.bpj.2022.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/02/2022] Open
Abstract
Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. A DNA sequence has intrinsic shape and flexibility features. While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. Overall, this study suggests that flexibility-guided DNA shape, and not merely the static shape, is a key unexplored component of the complex DNA-TF recognition code.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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38
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Rube HT, Rastogi C, Feng S, Kribelbauer JF, Li A, Becerra B, Melo LAN, Do BV, Li X, Adam HH, Shah NH, Mann RS, Bussemaker HJ. Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning. Nat Biotechnol 2022; 40:1520-1527. [PMID: 35606422 PMCID: PMC9546773 DOI: 10.1038/s41587-022-01307-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 04/04/2022] [Indexed: 01/02/2023]
Abstract
Protein-ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions. Here we describe a flexible machine learning method, called ProBound, that accurately defines sequence recognition in terms of equilibrium binding constants or kinetic rates. This is achieved using a multi-layered maximum-likelihood framework that models both the molecular interactions and the data generation process. We show that ProBound quantifies transcription factor (TF) behavior with models that predict binding affinity over a range exceeding that of previous resources; captures the impact of DNA modifications and conformational flexibility of multi-TF complexes; and infers specificity directly from in vivo data such as ChIP-seq without peak calling. When coupled with an assay called KD-seq, it determines the absolute affinity of protein-ligand interactions. We also apply ProBound to profile the kinetics of kinase-substrate interactions. ProBound opens new avenues for decoding biological networks and rationally engineering protein-ligand interactions.
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Affiliation(s)
- H Tomas Rube
- Department of Bioengineering, University of California, Merced, Merced, CA, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Allyson Li
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Basheer Becerra
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lucas A N Melo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Bach Viet Do
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Xiaoting Li
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Hammaad H Adam
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
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39
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Kshirsagar M, Yuan H, Ferres JL, Leslie C. BindVAE: Dirichlet variational autoencoders for de novo motif discovery from accessible chromatin. Genome Biol 2022; 23:174. [PMID: 35971180 PMCID: PMC9380350 DOI: 10.1186/s13059-022-02723-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
We present a novel unsupervised deep learning approach called BindVAE, based on Dirichlet variational autoencoders, for jointly decoding multiple TF binding signals from open chromatin regions. BindVAE can disentangle an input DNA sequence into distinct latent factors that encode cell-type specific in vivo binding signals for individual TFs, composite patterns for TFs involved in cooperative binding, and genomic context surrounding the binding sites. On the task of retrieving the motifs of expressed TFs in a given cell type, BindVAE is competitive with existing motif discovery approaches.
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Affiliation(s)
| | - Han Yuan
- Calico Life Sciences, South San Francisco, CA, USA
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40
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Comandante-Lou N, Baumann DG, Fallahi-Sichani M. AP-1 transcription factor network explains diverse patterns of cellular plasticity in melanoma cells. Cell Rep 2022; 40:111147. [PMID: 35926467 DOI: 10.1016/j.celrep.2022.111147] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/04/2022] [Accepted: 07/07/2022] [Indexed: 12/28/2022] Open
Abstract
Cellular plasticity associated with fluctuations in transcriptional programs allows individual cells in a tumor to adopt heterogeneous differentiation states and switch phenotype during their adaptive responses to therapies. Despite increasing knowledge of such transcriptional programs, the molecular basis of cellular plasticity remains poorly understood. Here, we combine multiplexed transcriptional and protein measurements at population and single-cell levels with multivariate statistical modeling to show that the state of AP-1 transcription factor network plays a unifying role in explaining diverse patterns of plasticity in melanoma. We find that a regulated balance among AP-1 factors cJUN, JUND, FRA2, FRA1, and cFOS determines the intrinsic diversity of differentiation states and adaptive responses to MAPK inhibitors in melanoma cells. Perturbing this balance through genetic depletion of specific AP-1 proteins, or by MAPK inhibitors, shifts cellular heterogeneity in a predictable fashion. Thus, AP-1 may serve as a critical node for manipulating cellular plasticity with potential therapeutic implications.
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Affiliation(s)
- Natacha Comandante-Lou
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Douglas G Baumann
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Mohammad Fallahi-Sichani
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; UVA Cancer Center, University of Virginia, Charlottesville, VA 22908, USA.
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41
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Zhang L, Wang L, Chen X, Zhao L, Liu X, Wang Y, Wu G, Xia C, Zhang L, Kong X. The protein phosphatase 2C clade A TaPP2CA interact with calcium-dependent protein kinases, TaCDPK5/TaCDPK9-1, that phosphorylate TabZIP60 transcription factor from wheat (Triticum aestivum L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111304. [PMID: 35696905 DOI: 10.1016/j.plantsci.2022.111304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/20/2022] [Accepted: 04/24/2022] [Indexed: 05/20/2023]
Abstract
Previously we have found that TabZIP60 from the ABF/AREB (ABRE-binding factor/ABA-responsive element-binding protein) subfamily of bZIP transcription factor (TF) was involved in salt stress response. However, the regulatory mechanism of TabZIP60 is unknown. In the present study, we identified two calcium-dependent protein kinase (CDPK) genes, TaCDPK5/TaCDPK9-1, which were clustered into group Ⅰ and were induced by salt, abscisic acid (ABA), and polyethylene glycol (PEG) treatments. RT-qPCR results showed that the expression level of salt-induced TabZIP60 was drastically inhibited by Ca2+ channel blocker LaCl3. TaCDPK5/TaCDPK9-1 were involved in interaction with TabZIP60 protein in vivo and in vitro. And TaCDPK5/TaCDPK9-1 could autophosphorylate and phosphorylate TabZIP60 protein in a Ca2+-dependent way. Mutational analysis indicated that Serine-110 of TabZIP60 was essential for TaCDPK5/TaCDPK9-1-TabZIP60 interaction and was the phosphorylation site of TaCDPK5/TaCDPK9-1 kinases. Yeast two-hybrid assay results showed the interactions between TaCDPK5/TaCDPK9-1 and wheat protein phosphatase 2 C clade A TaPP2CA116/ TaPP2CA121 separately. These findings demonstrate that the phosphorylation status of TabZIP60 controlled by TaPP2CA116/ TaPP2CA121 and TaCDPK5/TaCDPK9-1 might play a crucial role in wheat during salt stress.
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Affiliation(s)
- Lina Zhang
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu 730070, China.
| | - Liting Wang
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu 730070, China
| | - Xue Chen
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu 730070, China
| | - Lijuan Zhao
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu 730070, China
| | - Xingyan Liu
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu 730070, China
| | - Yinghong Wang
- Xinxiang Academy of Agricultural Sciences, Xinxiang, Henan 453000, China
| | - Guofan Wu
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu 730070, China
| | - Chuan Xia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lichao Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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42
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Tomaž Š, Gruden K, Coll A. TGA transcription factors-Structural characteristics as basis for functional variability. FRONTIERS IN PLANT SCIENCE 2022; 13:935819. [PMID: 35958211 PMCID: PMC9360754 DOI: 10.3389/fpls.2022.935819] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
TGA transcription factors are essential regulators of various cellular processes, their activity connected to different hormonal pathways, interacting proteins and regulatory elements. Belonging to the basic region leucine zipper (bZIP) family, TGAs operate by binding to their target DNA sequence as dimers through a conserved bZIP domain. Despite sharing the core DNA-binding sequence, the TGA paralogues exert somewhat different DNA-binding preferences. Sequence variability of their N- and C-terminal protein parts indicates their importance in defining TGA functional specificity through interactions with diverse proteins, affecting their DNA-binding properties. In this review, we provide a short and concise summary on plant TGA transcription factors from a structural point of view, including the relation of their structural characteristics to their functional roles in transcription regulation.
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Affiliation(s)
- Špela Tomaž
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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43
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Mun S, Han K, Hyun JK. The Time Sequence of Gene Expression Changes after Spinal Cord Injury. Cells 2022; 11:cells11142236. [PMID: 35883679 PMCID: PMC9324287 DOI: 10.3390/cells11142236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/15/2022] [Accepted: 07/17/2022] [Indexed: 02/01/2023] Open
Abstract
Gene expression changes following spinal cord injury (SCI) are time-dependent, and an accurate understanding of these changes can be crucial in determining time-based treatment options in a clinical setting. We performed RNA sequencing of the contused spinal cord of rats at five different time points from the very acute to chronic stages (1 hour, 1 day, 1 week, 1 month, and 3 months) following SCI. We identified differentially expressed genes (DEGs) and Gene Ontology (GO) terms at each time point, and 14,257 genes were commonly expressed at all time points. The biological process of the inflammatory response was increased at 1 hour and 1 day, and the cellular component of the integral component of the synaptic membrane was increased at 1 day. DEGs associated with cell activation and the innate immune response were highly enriched at 1 week and 1 month, respectively. A total of 2841 DEGs were differentially expressed at any of the five time points, and 18 genes (17 upregulated and 1 downregulated) showed common expression differences at all time points. We found that interleukin signaling, neutrophil degranulation, eukaryotic translation, collagen degradation, LGI–ADAM interactions, GABA receptor, and L1CAM-ankyrin interactions were prominent after SCI depending on the time post injury. We also performed gene–drug network analysis and found several potential antagonists and agonists which can be used to treat SCI. We expect to discover effective treatments in the clinical field through further studies revealing the efficacy and safety of potential drugs.
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Affiliation(s)
- Seyoung Mun
- Department of Nanobiomedical Science & BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea;
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea;
| | - Kyudong Han
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea;
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Jung Keun Hyun
- Department of Nanobiomedical Science & BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea;
- Department of Rehabilitation Medicine, College of Medicine, Dankook University, Cheonan 31116, Korea
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea
- Correspondence: ; Tel.: +82-10-2293-3415
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44
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Brennan A, Leech JT, Kad NM, Mason JM. An Approach to Derive Functional Peptide Inhibitors of Transcription Factor Activity. JACS AU 2022; 2:996-1006. [PMID: 35557753 PMCID: PMC9088798 DOI: 10.1021/jacsau.2c00105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 06/15/2023]
Abstract
We report the development of a high-throughput, intracellular "transcription block survival" (TBS) screening platform to derive functional transcription factor antagonists. TBS is demonstrated using the oncogenic transcriptional regulator cJun, with the development of antagonists that bind cJun and prevent both dimerization and, more importantly, DNA binding remaining a primary challenge. In TBS, cognate TRE sites are introduced into the coding region of the essential gene, dihydrofolate reductase (DHFR). Introduction of cJun leads to TRE binding, preventing DHFR expression by directly blocking RNA polymerase gene transcription to abrogate cell proliferation. Peptide library screening identified a sequence that both binds cJun and antagonizes function by preventing DNA binding, as demonstrated by restored cell viability and subsequent in vitro hit validation. TBS is an entirely tag-free genotype-to-phenotype approach, selecting desirable attributes such as high solubility, target specificity, and low toxicity within a complex cellular environment. TBS facilitates rapid library screening to accelerate the identification of therapeutically valuable sequences.
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Affiliation(s)
- Andrew Brennan
- Department
of Biology & Biochemistry, University
of Bath, Bath BA2 7AY, U.K.
| | - James T. Leech
- School
of Biosciences, University of Kent, Canterbury CT2 7NH, U.K.
| | - Neil M. Kad
- School
of Biosciences, University of Kent, Canterbury CT2 7NH, U.K.
| | - Jody M. Mason
- Department
of Biology & Biochemistry, University
of Bath, Bath BA2 7AY, U.K.
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45
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Katz HR, Arcese AA, Bloom O, Morgan JR. Activating Transcription Factor 3 (ATF3) is a Highly Conserved Pro-regenerative Transcription Factor in the Vertebrate Nervous System. Front Cell Dev Biol 2022; 10:824036. [PMID: 35350379 PMCID: PMC8957905 DOI: 10.3389/fcell.2022.824036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
The vertebrate nervous system exhibits dramatic variability in regenerative capacity across species and neuronal populations. For example, while the mammalian central nervous system (CNS) is limited in its regenerative capacity, the CNS of many other vertebrates readily regenerates after injury, as does the peripheral nervous system (PNS) of mammals. Comparing molecular responses across species and tissues can therefore provide valuable insights into both conserved and distinct mechanisms of successful regeneration. One gene that is emerging as a conserved pro-regenerative factor across vertebrates is activating transcription factor 3 (ATF3), which has long been associated with tissue trauma. A growing number of studies indicate that ATF3 may actively promote neuronal axon regrowth and regeneration in species ranging from lampreys to mammals. Here, we review data on the structural and functional conservation of ATF3 protein across species. Comparing RNA expression data across species that exhibit different abilities to regenerate their nervous system following traumatic nerve injury reveals that ATF3 is consistently induced in neurons within the first few days after injury. Genetic deletion or knockdown of ATF3 expression has been shown in mouse and zebrafish, respectively, to reduce axon regeneration, while inducing ATF3 promotes axon sprouting, regrowth, or regeneration. Thus, we propose that ATF3 may be an evolutionarily conserved regulator of neuronal regeneration. Identifying downstream effectors of ATF3 will be a critical next step in understanding the molecular basis of vertebrate CNS regeneration.
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Affiliation(s)
- Hilary R Katz
- The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Anthony A Arcese
- The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Ona Bloom
- The Feinstein Institutes for Medical Research, Manhasset, NY, United States.,The Donald and Barbara Zucker School of Medicine, Hempstead, NY, United States
| | - Jennifer R Morgan
- The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, United States
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46
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Knani I, Singh P, Gross-Cohen M, Aviram S, Ilan N, Sanderson RD, Aronheim A, Vlodavsky I. Induction of heparanase 2 (Hpa2) expression by stress is mediated by ATF3. Matrix Biol 2022; 105:17-30. [PMID: 34808335 PMCID: PMC8821145 DOI: 10.1016/j.matbio.2021.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 01/03/2023]
Abstract
Activity of heparanase, endoglycosidase that cleaves heparan sulfate side chains in heparan sulfate proteoglycans, is highly implicated in tumor progression and metastasis. Heparanase inhibitors are therefore being evaluated clinically as anti-cancer therapeutics. Heparanase 2 (Hpa2) is a close homolog of heparanase that lacks HS-degrading activity and functions as an endogenous inhibitor of heparanase. As a result, Hpa2 appears to attenuate tumor growth but mechanisms that regulate Hpa2 expression and determine the ratio between heparanase and Hpa2 are largely unknown. We have recently reported that the expression of Hpa2 is induced by endoplasmic reticulum (ER) and proteotoxic stresses, but the mechanism(s) underlying Hpa2 gene regulation was obscure. Here we expand the notion that Hpa2 is regulated by conditions of stress. We report that while ER and hypoxia, each alone, resulted in a 3-7 fold increase in Hpa2 expression, combining ER stress and hypoxia resulted in a noticeable, over 40-fold increase in Hpa2 expression. A prominent induction of Hpa2 expression was also quantified in cells exposed to heat shock, proteotoxic stress, lysosomal stress, and chemotherapy (cisplatin), strongly implying that Hpa2 is regulated by conditions of stress. Furthermore, analyses of the Hpa2 gene promoter led to the identification of activating-transcription-factor 3 (ATF3) as a transcription factor that mediates Hpa2 induction by stress, thus revealing, for the first time, a molecular mechanism that underlies Hpa2 gene regulation. Induction of Hpa2 and ATF3 by conditions of stress that often accompany the rapid expansion of tumors is likely translated to improved survival of cancer patients.
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Affiliation(s)
- Ibrahim Knani
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Preeti Singh
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Miriam Gross-Cohen
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Sharon Aviram
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Neta Ilan
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Ralph D Sanderson
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ami Aronheim
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Israel Vlodavsky
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel,Correspondence should be addressed: Israel Vlodavsky, Technion Integrated Cancer Center, Bruce Rappaport Faculty of Medicine; Technion, P. O. Box 9649, Haifa 31096, Israel,
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47
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Quiroz-Figueroa K, Vitali C, Conlon DM, Millar JS, Tobias JW, Bauer RC, Hand NJ, Rader DJ. TRIB1 regulates LDL metabolism through CEBPα-mediated effects on the LDL receptor in hepatocytes. J Clin Invest 2021; 131:146775. [PMID: 34779419 DOI: 10.1172/jci146775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 09/21/2021] [Indexed: 12/20/2022] Open
Abstract
Genetic variants near the TRIB1 gene are highly significantly associated with plasma lipid traits and coronary artery disease. While TRIB1 is likely causal of these associations, the molecular mechanisms are not well understood. Here we sought to investigate how TRIB1 influences low density lipoprotein cholesterol (LDL-C) levels in mice. Hepatocyte-specific deletion of Trib1 (Trib1Δhep) in mice increased plasma cholesterol and apoB and slowed the catabolism of LDL-apoB due to decreased levels of LDL receptor (LDLR) mRNA and protein. Simultaneous deletion of the transcription factor CCAAT/enhancer-binding protein alpha (CEBPα) with TRIB1 eliminated the effects of TRIB1 on hepatic LDLR regulation and LDL catabolism. Using RNA-seq, we found that activating transcription factor 3 (Atf3) was highly upregulated in the livers of Trib1Δhep but not Trib1Δhep CebpaΔhep mice. ATF3 has been shown to directly bind to the CEBPα protein, and to repress the expression of LDLR by binding its promoter. Blunting the increase of ATF3 in Trib1Δhep mice reduced the levels of plasma cholesterol and partially attenuated the effects on LDLR. Based on these data, we conclude that deletion of Trib1 leads to a posttranslational increase in CEBPα, which increases ATF3 levels, thereby contributing to the downregulation of LDLR and increased plasma LDL-C.
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Affiliation(s)
| | - Cecilia Vitali
- Division of Translational Medicine and Human Genetics, Department of Medicine
| | - Donna M Conlon
- Division of Translational Medicine and Human Genetics, Department of Medicine
| | - John S Millar
- Division of Translational Medicine and Human Genetics, Department of Medicine
| | | | - Robert C Bauer
- Division of Translational Medicine and Human Genetics, Department of Medicine
| | - Nicholas J Hand
- Department of Genetics.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel J Rader
- Division of Translational Medicine and Human Genetics, Department of Medicine.,Department of Genetics.,Department of Pediatrics, and.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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48
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Zheng Z, Aihemaiti Y, Liu J, Afridi MI, Yang S, Zhang X, Xu Y, Chen C, Tu H. The bZIP Transcription Factor ZIP-11 Is Required for the Innate Immune Regulation in Caenorhabditis elegans. Front Immunol 2021; 12:744454. [PMID: 34804026 PMCID: PMC8602821 DOI: 10.3389/fimmu.2021.744454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
Innate immunity is the first line of host defense against pathogen infection in metazoans. However, the molecular mechanisms of the complex immune regulatory network are not fully understood. Based on a transcriptome profiling of the nematode Caenorhabditis elegans, we found that a bZIP transcription factor ZIP-11 was up-regulated upon Pseudomonas aeruginosa PA14 infection. The tissue specific RNAi knock-down and rescue data revealed that ZIP-11 acts in intestine to promote host resistance against P. aeruginosa PA14 infection. We further showed that intestinal ZIP-11 regulates innate immune response through constituting a feedback loop with the conserved PMK-1/p38 mitogen-activated protein signaling pathway. Intriguingly, ZIP-11 interacts with a CCAAT/enhancer-binding protein, CEBP-2, to mediate the transcriptional response to P. aeruginosa PA14 infection independently of PMK-1/p38 pathway. In addition, human homolog ATF4 can functionally substitute for ZIP-11 in innate immune regulation of C. elegans. Our findings indicate that the ZIP-11/ATF4 genetic program activates local innate immune response through conserved PMK-1/p38 and CEBP-2/C/EBPγ immune signals in C. elegans, raising the possibility that a similar process may occur in other organisms.
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Affiliation(s)
- Zhongfan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Yilixiati Aihemaiti
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Junqiang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Muhammad Irfan Afridi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Shengmei Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Xiumei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Yongfu Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Chunhong Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Haijun Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
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49
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Mason MRJ, Erp S, Wolzak K, Behrens A, Raivich G, Verhaagen J. The Jun-dependent axon regeneration gene program: Jun promotes regeneration over plasticity. Hum Mol Genet 2021; 31:1242-1262. [PMID: 34718572 PMCID: PMC9029231 DOI: 10.1093/hmg/ddab315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
The regeneration-associated gene (RAG) expression program is activated in injured peripheral neurons after axotomy and enables long-distance axon re-growth. Over 1000 genes are regulated, and many transcription factors are upregulated or activated as part of this response. However, a detailed picture of how RAG expression is regulated is lacking. In particular, the transcriptional targets and specific functions of the various transcription factors are unclear. Jun was the first-regeneration-associated transcription factor identified and the first shown to be functionally important. Here we fully define the role of Jun in the RAG expression program in regenerating facial motor neurons. At 1, 4 and 14 days after axotomy, Jun upregulates 11, 23 and 44% of the RAG program, respectively. Jun functions relevant to regeneration include cytoskeleton production, metabolic functions and cell activation, and the downregulation of neurotransmission machinery. In silico analysis of promoter regions of Jun targets identifies stronger over-representation of AP1-like sites than CRE-like sites, although CRE sites were also over-represented in regions flanking AP1 sites. Strikingly, in motor neurons lacking Jun, an alternative SRF-dependent gene expression program is initiated after axotomy. The promoters of these newly expressed genes exhibit over-representation of CRE sites in regions near to SRF target sites. This alternative gene expression program includes plasticity-associated transcription factors and leads to an aberrant early increase in synapse density on motor neurons. Jun thus has the important function in the early phase after axotomy of pushing the injured neuron away from a plasticity response and towards a regenerative phenotype.
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Affiliation(s)
- Matthew R J Mason
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105, BA, Amsterdam, The Netherlands
| | - Susan Erp
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105, BA, Amsterdam, The Netherlands
| | - Kim Wolzak
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105, BA, Amsterdam, The Netherlands
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Gennadij Raivich
- UCL Institute for Women's Health, Maternal and Fetal Medicine, Perinatal Brain Repair Group, London, WC1E 6HX, United Kingdom
| | - Joost Verhaagen
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105, BA, Amsterdam, The Netherlands.,Center for Neurogenomics and Cognition Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, 1081HV, Amsterdam, The Netherlands
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50
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Li X, Gracilla D, Cai L, Zhang M, Yu X, Chen X, Zhang J, Long X, Ding HF, Yan C. ATF3 promotes the serine synthesis pathway and tumor growth under dietary serine restriction. Cell Rep 2021; 36:109706. [PMID: 34551291 PMCID: PMC8491098 DOI: 10.1016/j.celrep.2021.109706] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 07/23/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
The serine synthesis pathway (SSP) involving metabolic enzymes phosphoglycerate dehydrogenase (PHGDH), phosphoserine aminotransferase 1 (PSAT1), and phosphoserine phosphatase (PSPH) drives intracellular serine biosynthesis and is indispensable for cancer cells to grow in serine-limiting environments. However, how SSP is regulated is not well understood. Here, we report that activating transcription factor 3 (ATF3) is crucial for transcriptional activation of SSP upon serine deprivation. ATF3 is rapidly induced by serine deprivation via a mechanism dependent on ATF4, which in turn binds to ATF4 and increases the stability of this master regulator of SSP. ATF3 also binds to the enhancers/promoters of PHGDH, PSAT1, and PSPH and recruits p300 to promote expression of these SSP genes. As a result, loss of ATF3 expression impairs serine biosynthesis and the growth of cancer cells in the serine-deprived medium or in mice fed with a serine/glycine-free diet. Interestingly, ATF3 expression positively correlates with PHGDH expression in a subset of TCGA cancer samples. Activation of the serine synthesis pathway is important for cancer cell growth, but how this pathway is regulated is not well understood. Li et al. report that ATF3 is an important regulator of this pathway and can promote serine biosynthesis and tumor growth under serine-limiting conditions.
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Affiliation(s)
- Xingyao Li
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Daniel Gracilla
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Lun Cai
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Mingyi Zhang
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA; Institute of Materia Medica, Peking Union Medical College, Beijing 100050, China
| | - Xiaolin Yu
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Xiaoguang Chen
- Institute of Materia Medica, Peking Union Medical College, Beijing 100050, China
| | - Junran Zhang
- Department of Radiation Oncology, Ohio State University James Comprehensive Cancer Center and College of Medicine, Columbus, OH 43210, USA
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Han-Fei Ding
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
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