1
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [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: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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2
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Janssen BDE, van den Boogaard MJH, Lichtenbelt K, Seaby EG, Stals K, Ellard S, Newbury-Ecob R, Dixit A, Roht L, Pajusalu S, Õunap K, Firth HV, Buckley M, Wilson M, Roscioli T, Tidwell T, Mao R, Ennis S, Holwerda SJ, van Gassen K, van Jaarsveld RH. De novo putative loss-of-function variants in TAF4 are associated with a neuro-developmental disorder. Hum Mutat 2022; 43:1844-1851. [PMID: 35904126 PMCID: PMC10087332 DOI: 10.1002/humu.24444] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 01/24/2023]
Abstract
TATA-binding protein associated factor 4 (TAF4) is a subunit of the Transcription Factor IID (TFIID) complex, a central player in transcription initiation. Other members of this multimeric complex have been implicated previously as monogenic disease genes in human developmental disorders. TAF4 has not been described to date as a monogenic disease gene. We here present a cohort of eight individuals, each carrying de novo putative loss-of-function (pLoF) variants in TAF4 and expressing phenotypes consistent with a neuro-developmental disorder (NDD). Common features include intellectual disability, abnormal behavior, and facial dysmorphisms. We propose TAF4 as a novel dominant disease gene for NDD, and coin this novel disorder "TAF4-related NDD" (T4NDD). We place T4NDD in the context of other disorders related to TFIID subunits, revealing shared features of T4NDD with other TAF-opathies.
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Affiliation(s)
- Beau D E Janssen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Klaske Lichtenbelt
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eleanor G Seaby
- Genomic Informatics Group, University of Southampton, Southampton, UK
| | - Karen Stals
- Exeter Genomic Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Exeter Genomic Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Ruth Newbury-Ecob
- Clinical Genetics, St Michael's Hospital Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Abhijit Dixit
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Laura Roht
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | | | - Michael Buckley
- Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, and Discipline of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Tony Roscioli
- Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia.,Neurosciences Research Australia, University of NSW, Kensington, New South Wales, Australia.,Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | | | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Sarah Ennis
- Genomic Informatics Group, University of Southampton, Southampton, UK
| | - Sjoerd J Holwerda
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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3
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Bugge K, Staby L, Salladini E, Falbe-Hansen RG, Kragelund BB, Skriver K. αα-Hub domains and intrinsically disordered proteins: A decisive combo. J Biol Chem 2021; 296:100226. [PMID: 33361159 PMCID: PMC7948954 DOI: 10.1074/jbc.rev120.012928] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023] Open
Abstract
Hub proteins are central nodes in protein-protein interaction networks with critical importance to all living organisms. Recently, a new group of folded hub domains, the αα-hubs, was defined based on a shared αα-hairpin supersecondary structural foundation. The members PAH, RST, TAFH, NCBD, and HHD are found in large proteins such as Sin3, RCD1, TAF4, CBP, and harmonin, which organize disordered transcriptional regulators and membrane scaffolds in interactomes of importance to human diseases and plant quality. In this review, studies of structures, functions, and complexes across the αα-hubs are described and compared to provide a unified description of the group. This analysis expands the associated molecular concepts of "one domain-one binding site", motif-based ligand binding, and coupled folding and binding of intrinsically disordered ligands to additional concepts of importance to signal fidelity. These include context, motif reversibility, multivalency, complex heterogeneity, synergistic αα-hub:ligand folding, accessory binding sites, and supramodules. We propose that these multifaceted protein-protein interaction properties are made possible by the characteristics of the αα-hub fold, including supersite properties, dynamics, variable topologies, accessory helices, and malleability and abetted by adaptability of the disordered ligands. Critically, these features provide additional filters for specificity. With the presentations of new concepts, this review opens for new research questions addressing properties across the group, which are driven from concepts discovered in studies of the individual members. Combined, the members of the αα-hubs are ideal models for deconvoluting signal fidelity maintained by folded hubs and their interactions with intrinsically disordered ligands.
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Affiliation(s)
- Katrine Bugge
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Staby
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edoardo Salladini
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus G Falbe-Hansen
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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4
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Xiong J, Feng Z, Li Z, Zhong T, Yang Z, Tu Y, Xiao T, Jie Z, Cao Y. Overexpression of TWA1 predicts poor prognosis in patients with gastric cancer. Pathol Res Pract 2019; 215:152594. [PMID: 31591053 DOI: 10.1016/j.prp.2019.152594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 07/24/2019] [Accepted: 08/16/2019] [Indexed: 01/07/2023]
Abstract
TWA1 is associated with microtubule dynamics, cell migration, nucleokinesis and chromosome segregation. However, the role of TWA1 in gastric cancer (GC) remains unclear. In this study, Cosmic database revealed that the expression level of TWA1 ranks in the top 20 of overexpressed genes in GC. Further bioinformatic analysis revealed that the expression level of TWA1 was not in connection with the infection status of HP or EB. IHC and IF showed that TWA1 protein was present in both the cytoplasm and nucleus, but mainly in the cytoplasm. The high expression level of TWA1 was also related to tumor size, depth of invasion, lymph node metastasis, TNM stage, cancerous node and vascular invasion. Furthermore, higher TWA1 expression was also associated with shorter PFS and OS in GC. The univariate and multivariate analysis suggested the expression of TWA1 was an independent poor prognostic factor in GC. DNA copy number gain contributes to TWA1 overexpression and promoter methylation of TWA1 predicts profitable prognosis. Co-expression showed that TAF4 may function as a transcription factor (TF) regulates TWA1 expression, which further to mediate tumor invasion and metastasis. These findings revealed that TWA1 plays an important role in the development of GC and is expected to become an important biomarker and therapeutic target of tumors.
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Affiliation(s)
- Jianbo Xiong
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Zongfeng Feng
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Zhengrong Li
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China.
| | - Tao Zhong
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Zhouwen Yang
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yi Tu
- Department of Pathology, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Tao Xiao
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Zhigang Jie
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yi Cao
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China.
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5
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Chen L, Huang T, Qiao Y, Jiang F, Lan J, Zhou Y, Yang C, Yan S, Luo K, Su L, Li J. Perspective into
the regulation of cell‐generated forces toward stem cell migration and differentiation. J Cell Biochem 2018; 120:8884-8890. [PMID: 30536423 DOI: 10.1002/jcb.28251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/22/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Liujing Chen
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Tu Huang
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Yini Qiao
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Fulin Jiang
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Jingxiang Lan
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Yimei Zhou
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Cai Yang
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Shanyu Yan
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Kaihui Luo
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Liping Su
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
| | - Juan Li
- State Key Laboratory of Oral Diseases Department of Orthodontics, West China Hospital of Stomatology West China School of Stomatology, Sichuan University Chengdu Sichuan China
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6
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Hueso M, De Ramon L, Navarro E, Ripoll E, Cruzado JM, Grinyo JM, Torras J. Silencing of CD40 in vivo reduces progression of experimental atherogenesis through an NF-κB/miR-125b axis and reveals new potential mediators in the pathogenesis of atherosclerosis. Atherosclerosis 2016; 255:80-89. [DOI: 10.1016/j.atherosclerosis.2016.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 10/06/2016] [Accepted: 11/01/2016] [Indexed: 02/08/2023]
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7
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Abstract
Here, I argue that some of the secrets of complex biological function rely on assemblies of many heterogeneous proteins that together enable sophisticated sensing and actuating processes. Evolution seems to delight in making these structures and in continually elaborating upon their capabilities. Developing tools that can go beyond the few protein limit, both on the experimental frontier and from a theoretical, conceptual framework, should be an extremely high priority for the next generation of molecular biophysicists.
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Affiliation(s)
- Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
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8
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Kazantseva J, Sadam H, Neuman T, Palm K. Targeted alternative splicing of TAF4: a new strategy for cell reprogramming. Sci Rep 2016; 6:30852. [PMID: 27499390 PMCID: PMC4976350 DOI: 10.1038/srep30852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/08/2016] [Indexed: 12/20/2022] Open
Abstract
Reprogramming of somatic cells has become a versatile tool for biomedical research and for regenerative medicine. In the current study, we show that manipulating alternative splicing (AS) is a highly potent strategy to produce cells for therapeutic applications. We demonstrate that silencing of hTAF4-TAFH activity of TAF4 converts human facial dermal fibroblasts to melanocyte-like (iMel) cells. iMel cells produce melanin and express microphthalmia-associated transcription factor (MITF) and its target genes at levels comparable to normal melanocytes. Reprogramming of melanoma cells by manipulation with hTAF4-TAFH activity upon TAFH RNAi enforces cell differentiation towards chondrogenic pathway, whereas ectoptic expression of TAF4 results in enhanced multipotency and neural crest-like features in melanoma cells. In both cell states, iMels and cancer cells, hTAF4-TAFH activity controls migration by supporting E- to N-cadherin switches. From our data, we conclude that targeted splicing of hTAF4-TAFH coordinates AS of other TFIID subunits, underscoring the role of TAF4 in synchronised changes of Pol II complex composition essential for efficient cellular reprogramming. Taken together, targeted AS of TAF4 provides a unique strategy for generation of iMels and recapitulating stages of melanoma progression.
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Affiliation(s)
| | - Helle Sadam
- Protobios LLC, Tallinn, Estonia.,The Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | | | - Kaia Palm
- Protobios LLC, Tallinn, Estonia.,The Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
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9
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Shao Y, Qiao L, Wu L, Sun X, Zhu D, Yang G, Zhang X, Mao X, Chen W, Liang W, Zhang Y, Zhang L. Structure Identification and Anti-Cancer Pharmacological Prediction of Triterpenes from Ganoderma lucidum. Molecules 2016; 21:E678. [PMID: 27213329 PMCID: PMC6273610 DOI: 10.3390/molecules21050678] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 05/16/2016] [Accepted: 05/19/2016] [Indexed: 11/17/2022] Open
Abstract
Ganoderma triterpenes (GTs) are the major secondary metabolites of Ganoderma lucidum, which is a popularly used traditional Chinese medicine for complementary cancer therapy. In the present study, systematic isolation, and in silico pharmacological prediction are implemented to discover potential anti-cancer active GTs from G. lucidum. Nineteen GTs, three steroids, one cerebroside, and one thymidine were isolated from G. lucidum. Six GTs were first isolated from the fruiting bodies of G. lucidum, including 3β,7β,15β-trihydroxy-11,23-dioxo-lanost-8,16-dien-26-oic acid methyl ester (1), 3β,7β,15β-trihydroxy-11,23-dioxo-lanost-8,16-dien-26-oic acid (2), 3β,7β,15α,28-tetrahydroxy-11,23-dioxo-lanost-8,16-dien-26-oic acid (3), ganotropic acid (4), 26-nor-11,23-dioxo-5α-lanost-8-en-3β,7β,15α,25-tetrol (5) and (3β,7α)-dihydroxy-lanosta-8,24-dien- 11-one (6). (4E,8E)-N-d-2'-hydroxypalmitoyl-l-O-β-d-glucopyranosyl-9-methyl-4,8-spingodienine (7), and stigmasta-7,22-dien-3β,5α,6α-triol (8) were first reported from the genus Ganodema. By using reverse pharmacophoric profiling of the six GTs, thirty potential anti-cancer therapeutic targets were identified and utilized to construct their ingredient-target interaction network. Then nineteen high frequency targets of GTs were selected from thirty potential targets to construct a protein interaction network (PIN). In order to cluster the pharmacological activity of GTs, twelve function modules were identified by molecular complex detection (MCODE) and gene ontology (GO) enrichment analysis. The results indicated that anti-cancer effect of GTs might be related to histone acetylation and interphase of mitotic cell cycle by regulating general control non-derepressible 5 (GCN5) and cyclin-dependent kinase-2 (CDK2), respectively. This research mode of extraction, isolation, pharmacological prediction, and PIN analysis might be beneficial to rapidly predict and discover pharmacological activities of novel compounds.
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Affiliation(s)
- Yanyan Shao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Liansheng Qiao
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Lingfang Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Xuefei Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Dan Zhu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Guanghui Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Xiaoxue Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Xin Mao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Wenjing Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Wenyi Liang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yanling Zhang
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Lanzhen Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
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