1
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Pan L, Zhu F, Yu A, Jia C, Tang H, Zhou M, Li M, Jiang S, Li J, Cui Y, Tang L. Effect of bromodomain PHD-finger transcription factor (BPTF) on trophoblast epithelial-to-mesenchymal transition. Gene 2024; 914:148405. [PMID: 38521110 DOI: 10.1016/j.gene.2024.148405] [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: 12/17/2023] [Revised: 03/03/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
The trophoblast epithelial-to-mesenchymal transition (EMT) is a procedure related to embryo implantation, spiral artery establishment and fetal-maternal communication, which is a key event for successful pregnancy. Inadequate EMT is one of the pathological mechanisms of recurrent miscarriage (RM). Whole-exome sequencing revealed that the mutation of bromodomain PHD-finger transcription factor (BPTF) was strongly associated with RM. In the present study, the effects of BPTF on EMT and the underlying mechanism were investigated. We found that the expression of BPTF in the villi of RM patients was significantly downregulated. Gene Ontology (GO) analysis revealed that BPTF participated in cell adhesion. The knockdown of BPTF prevented EMT and attenuated trophoblast invasion in vitro. BPTF activated Slug transcription by binding directly to the promoter region of the Slug gene. Interestingly, the protein levels of both Slug and BPTF were decreased in the villous cytotrophoblasts (VCTs) of RM villi. In conclusion, BPTF participates in the regulation of trophoblast EMT by activating Slug expression, suggesting that BPTF defects are an important factor in RM pathogenesis.
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Affiliation(s)
- Linqing Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Clinical Center of Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, Kangda College of Nanjing Medical University, Lianyungang 222000, China
| | - Fuquan Zhu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Aochen Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Jia
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huaiyun Tang
- Clinical Center of Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, Kangda College of Nanjing Medical University, Lianyungang 222000, China
| | - Minglian Zhou
- Clinical Center of Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, Kangda College of Nanjing Medical University, Lianyungang 222000, China
| | - Mingrui Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center of Clinical Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shiwen Jiang
- Clinical Center of Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, Kangda College of Nanjing Medical University, Lianyungang 222000, China
| | - Juan Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yugui Cui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center of Clinical Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
| | - Lisha Tang
- Clinical Center of Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, Kangda College of Nanjing Medical University, Lianyungang 222000, China.
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2
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Xia Z, Ding X, Ji C, Zhou D, Sun X, Liu T. EP300 restores the glycolytic activity and anti-tumor function of CD8 + cytotoxic T cells in nasopharyngeal carcinoma. iScience 2024; 27:108957. [PMID: 38333692 PMCID: PMC10850748 DOI: 10.1016/j.isci.2024.108957] [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: 04/04/2023] [Revised: 08/30/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Competition for glucose may metabolically limit T cells during cancer progression. This study shows that culturing in the condition medium (CM) of NPC c6661 cells restricted glycolytic and immune activities of CD8+ T cells. These cells also exhibited limited tumor-eliminating effects in mouse xenograft tumor models. Glucose supplementation restored glycolysis and immune activity of CD8+ T cells in vitro and in vivo by rescuing the expression of E1A binding protein p300 (EP300). EP300 upregulated bromodomain PHD finger transcription factor (BPTF) expression by catalyzing H3K27ac modification, and BPTF further activated AT-rich interaction domain 1A (ARID1A) transcription. Either BPTF or ARID1A knockdown in CD8+ T cells reduced their glycolytic activity, decreased the secretion of cytotoxic molecules, and blocked the tumor-killing function in mice. Overall, this study demonstrates that EP300 restores the glycolytic and anti-tumor activities of CD8+ T cells in the glucose restriction condition in NPC through the BPTF/ARID1A axis.
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Affiliation(s)
- Zhixiu Xia
- Colorectal Tumor Surgery Ward, Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, P.R. China
| | - Xiaoxu Ding
- Department of Otorhinolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, P.R. China
| | - Chao Ji
- Clinical Epidemiology Teaching and Research Section, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, P.R. China
| | - Dabo Zhou
- Repair Teaching and Research Section, School and Hospital of Stomatology, China Medical University, Shenyang 110002, Liaoning, P.R. China
| | - Xun Sun
- Department of Immunology, College of Basic Medicine, China Medical University, Shenyang 110002, Liaoning, P.R. China
| | - Tiancong Liu
- Department of Otorhinolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, P.R. China
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3
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Wang D, Lu X, Jiang Y, Pan L, Zhu F, Yu A, Zhao M, Yang M, Bi J, He X, Liu H, Li J. The chromatin remodeling protein BPTF mediates cell cycle, proliferation and apoptosis in porcine ovarian granulosa cells. Theriogenology 2023; 211:172-181. [PMID: 37643502 DOI: 10.1016/j.theriogenology.2023.08.017] [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: 04/07/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Bromodomain PHD finger transcription factor (BPTF), a core subunit of nucleosome-remodeling factor (NURF) complex, plays an important role in chromatin remodeling. However, few information of BPTF is available in pig, especially in mammalian follicular granulosa cells (GCs). The present study firstly confirmed that BPTF in porcine was relative close to human and mouse. The expression of BPTF could be detected in ovary, testes, lung, kidney, large intestine, and small intestine. And a relative high expression of BPTF was observed in ovarian follicles and GCs. When BPTF was knocked down (BPTF-siRNA), the viability of GCs was affected. And the expression level of CDK1, cyclin B1, CDK4 and CDK2 was higher than the control, which might indicate that the cell cycle of GCs was inhibited from S to G2/M phase. Although the apoptosis level was induced in the BPTF-siRNA GCs, the reduced level of H3K4 methylation was detected with the down regulation of SMYD3, EHMT2 and DPY30. Thereby, results in the present might provide the primary knowledge of BPTF in GCs and the follicular development in pig.
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Affiliation(s)
- Dayu Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinyue Lu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuan Jiang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Linqing Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fuquan Zhu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Aochen Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mingyue Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Meng Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jiaying Bi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xu He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Juan Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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4
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Picketts D, Mirzaa G, Yan K, Relator R, Timpano S, Yalcin B, Collins S, Ziegler A, Pao E, Oyama N, Brischoux-Boucher E, Piard J, Monaghan K, Sacoto MG, Dobyns W, Park K, Fernández-Mayoralas D, Fernández-Jaén A, Jayakar P, Brusco A, Antona V, Giorgio E, Kvarnung M, Isidor B, Conrad S, Cogné B, Deb W, Stuurman KE, Sterbova K, Smal N, Weckhuysen S, Oegema R, Innes M, Latsko M, Ben-Omran T, Yeh R, Kruer M, Bakhtiari S, Papavasiliou A, Moutton S, Nambot S, Chanprasert S, Paolucci S, Miller K, Burton B, Kim K, O'Heir E, Bruwer Z, Donald K, Kleefstra T, Goldstein A, Angle B, Bontempo K, Miny P, Joset P, Demurger F, Hobson E, Pang L, Carpenter L, Li D, Bonneau D, Sadikovic B. Pathogenic variants in SMARCA1 cause an X-linked neurodevelopmental disorder modulated by NURF complex composition. RESEARCH SQUARE 2023:rs.3.rs-3317938. [PMID: 37841849 PMCID: PMC10571636 DOI: 10.21203/rs.3.rs-3317938/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Pathogenic variants in ATP-dependent chromatin remodeling proteins are a recurrent cause of neurodevelopmental disorders (NDDs). The NURF complex consists of BPTF and either the SNF2H (SMARCA5) or SNF2L (SMARCA1) ISWI-chromatin remodeling enzyme. Pathogenic variants in BPTF and SMARCA5 were previously implicated in NDDs. Here, we describe 40 individuals from 30 families with de novo or maternally inherited pathogenic variants in SMARCA1. This novel NDD was associated with mild to severe ID/DD, delayed or regressive speech development, and some recurrent facial dysmorphisms. Individuals carrying SMARCA1 loss-of-function variants exhibited a mild genome-wide DNA methylation profile and a high penetrance of macrocephaly. Genetic dissection of the NURF complex using Smarca1, Smarca5, and Bptfsingle and double mouse knockouts revealed the importance of NURF composition and dosage for proper forebrain development. Finally, we propose that genetic alterations affecting different NURF components result in a NDD with a broad clinical spectrum.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Emily Pao
- Seattle Children's Research Institute
| | | | | | | | | | | | | | - Kristen Park
- University of Colorado Denver School of Medicine
| | | | - Alberto Fernández-Jaén
- Department of Pediatrics and Neurology, Hospital Universitario Quirónsalud, School of Medicine, Universidad Europea de Madrid
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital
| | | | | | | | | | | | | | | | | | - K E Stuurman
- Department of Clinical Genetics, Erasmus University Medical Center
| | | | | | | | | | | | - Maeson Latsko
- The Steve and Cindy Rasmussen Institute for Genomic Medicine
| | | | | | | | | | | | | | - Sophie Nambot
- Centre de Génétique et Centre de référence «Anomalies du Développement et Syndromes Malformatifs», Hôpital d'Enfants, Centre Hospitalier
| | | | | | | | | | | | | | | | - Kirsten Donald
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Klipfontein Road/Private Bag, Rondebosch, 7700/7701, Cape Town, South A
| | | | | | | | | | | | | | | | | | | | | | - Dong Li
- The Children's Hospital of Philadelphia
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000
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5
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Zapata G, Yan K, Picketts DJ. Generation of a mouse model of the neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) syndrome. Hum Mol Genet 2022; 31:3405-3421. [PMID: 35604347 DOI: 10.1093/hmg/ddac119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Heterozygous variants in BPTF cause the neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) syndrome (MIM#617755) characterized by intellectual disability (ID), speech delay, and postnatal microcephaly. BPTF functions within NURF, a complex comprising SNF2L, an ISWI chromatin remodeling protein encoded by the SMARCA1 gene. Surprisingly, ablation of Smarca1 resulted in mice with enlarged brains, a direct contrast to the phenotype of NEDDFL patients. To model the NEDDFL syndrome, we generated forebrain-specific Bptf knockout (Bptf cKO) mice. Bptf cKO mice were born in normal Mendelian ratios, survived to adulthood but were smaller in size with severe cortical hypoplasia. Prolonged progenitor cell cycle length and a high incidence of cell death reduced neuronal output. Cortical lamination was also disrupted with reduced proportions of deep layer neurons, and neuronal maturation defects that impaired the acquisition of distinct cell fates (eg. Ctip2+ neurons). RNAseq and pathway analysis identified altered expression of fate-determining transcription factors, and biological pathways involved in neural development, apoptotic signaling, and amino acid biosynthesis. Dysregulated genes were enriched for Myc binding sites, a known BPTF transcriptional co-factor. We propose Bptf cKO mice as a valuable model for further study of the NEDDFL syndrome.
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Affiliation(s)
- Gerardo Zapata
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6.,Departments of Biochemistry, Microbiology, & Immunology, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6.,Departments of Biochemistry, Microbiology, & Immunology, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5.,Departments of Biochemistry, Microbiology, & Immunology, Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5.,Medicine, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5
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6
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Li Y, Gong H, Wang P, Zhu Y, Peng H, Cui Y, Li H, Liu J, Wang Z. The emerging role of ISWI chromatin remodeling complexes in cancer. J Exp Clin Cancer Res 2021; 40:346. [PMID: 34736517 PMCID: PMC8567610 DOI: 10.1186/s13046-021-02151-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Disordered chromatin remodeling regulation has emerged as an essential driving factor for cancers. Imitation switch (ISWI) family are evolutionarily conserved ATP-dependent chromatin remodeling complexes, which are essential for cellular survival and function through multiple genetic and epigenetic mechanisms. Omics sequencing and a growing number of basic and clinical studies found that ISWI family members displayed widespread gene expression and genetic status abnormalities in human cancer. Their aberrant expression is closely linked to patient outcome and drug response. Functional or componential alteration in ISWI-containing complexes is critical for tumor initiation and development. Furthermore, ISWI-non-coding RNA regulatory networks and some non-coding RNAs derived from exons of ISWI member genes play important roles in tumor progression. Therefore, unveiling the transcriptional regulation mechanism underlying ISWI family sparked a booming interest in finding ISWI-based therapies in cancer. This review aims at describing the current state-of-the-art in the role of ISWI subunits and complexes in tumorigenesis, tumor progression, immunity and drug response, and presenting deep insight into the physiological and pathological implications of the ISWI transcription machinery in cancers.
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Affiliation(s)
- Yanan Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Han Gong
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Pan Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yajuan Cui
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Heng Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
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7
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Zahid H, Olson NM, Pomerantz WCK. Opportunity knocks for uncovering the new function of an understudied nucleosome remodeling complex member, the bromodomain PHD finger transcription factor, BPTF. Curr Opin Chem Biol 2021; 63:57-67. [PMID: 33706239 PMCID: PMC8384639 DOI: 10.1016/j.cbpa.2021.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 12/27/2022]
Abstract
Nucleosome remodeling provides access to genomic DNA for recruitment of the transcriptional machinery to mediate gene expression. The aberrant function of nucleosome remodeling complexes has been correlated to human cancer, making them emerging therapeutic targets. The bromodomain PHD finger transcription factor, BPTF, is the largest member of the human nucleosome remodeling factor NURF. Over the last five years, BPTF has become increasingly identified as a protumorigenic factor, prompting investigations into the molecular mechanisms associated with BPTF function. Despite a druggable bromodomain, small molecule discovery is at an early stage. Here we highlight recent investigations into the biology being discovered for BPTF, chemical biology approaches used to study its function, and small molecule inhibitors being designed as future chemical probes and therapeutics.
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Affiliation(s)
- Huda Zahid
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Noelle M Olson
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - William C K Pomerantz
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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8
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Goodwin LR, Zapata G, Timpano S, Marenger J, Picketts DJ. Impaired SNF2L Chromatin Remodeling Prolongs Accessibility at Promoters Enriched for Fos/Jun Binding Sites and Delays Granule Neuron Differentiation. Front Mol Neurosci 2021; 14:680280. [PMID: 34295220 PMCID: PMC8290069 DOI: 10.3389/fnmol.2021.680280] [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: 03/13/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
Chromatin remodeling proteins utilize the energy from ATP hydrolysis to mobilize nucleosomes often creating accessibility for transcription factors within gene regulatory elements. Aberrant chromatin remodeling has diverse effects on neuroprogenitor homeostasis altering progenitor competence, proliferation, survival, or cell fate. Previous work has shown that inactivation of the ISWI genes, Smarca5 (encoding Snf2h) and Smarca1 (encoding Snf2l) have dramatic effects on brain development. Smarca5 conditional knockout mice have reduced progenitor expansion and severe forebrain hypoplasia, with a similar effect on the postnatal growth of the cerebellum. In contrast, Smarca1 mutants exhibited enlarged forebrains with delayed progenitor differentiation and increased neuronal output. Here, we utilized cerebellar granule neuron precursor (GNP) cultures from Smarca1 mutant mice (Ex6DEL) to explore the requirement for Snf2l on progenitor homeostasis. The Ex6DEL GNPs showed delayed differentiation upon plating that was not attributed to changes in the Sonic Hedgehog pathway but was associated with overexpression of numerous positive effectors of proliferation, including targets of Wnt activation. Transcriptome analysis identified increased expression of Fosb and Fosl2 while ATACseq experiments identified a large increase in chromatin accessibility at promoters many enriched for Fos/Jun binding sites. Nonetheless, the elevated proliferation index was transient and the Ex6DEL cultures initiated differentiation with a high concordance in gene expression changes to the wild type cultures. Genes specific to Ex6DEL differentiation were associated with an increased activation of the ERK signaling pathway. Taken together, this data provides the first indication of how Smarca1 mutations alter progenitor cell homeostasis and contribute to changes in brain size.
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Affiliation(s)
- Laura R Goodwin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Gerardo Zapata
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Sara Timpano
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jacob Marenger
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
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9
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Slepicka PF, Somasundara AVH, Dos Santos CO. The molecular basis of mammary gland development and epithelial differentiation. Semin Cell Dev Biol 2021; 114:93-112. [PMID: 33082117 PMCID: PMC8052380 DOI: 10.1016/j.semcdb.2020.09.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of the molecular events underpinning the development of mammalian organ systems has been increasing rapidly in recent years. With the advent of new and improved next-generation sequencing methods, we are now able to dig deeper than ever before into the genomic and epigenomic events that play critical roles in determining the fates of stem and progenitor cells during the development of an embryo into an adult. In this review, we detail and discuss the genes and pathways that are involved in mammary gland development, from embryogenesis, through maturation into an adult gland, to the role of pregnancy signals in directing the terminal maturation of the mammary gland into a milk producing organ that can nurture the offspring. We also provide an overview of the latest research in the single-cell genomics of mammary gland development, which may help us to understand the lineage commitment of mammary stem cells (MaSCs) into luminal or basal epithelial cells that constitute the mammary gland. Finally, we summarize the use of 3D organoid cultures as a model system to study the molecular events during mammary gland development. Our increased investigation of the molecular requirements for normal mammary gland development will advance the discovery of targets to predict breast cancer risk and the development of new breast cancer therapies.
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Affiliation(s)
- Priscila Ferreira Slepicka
- Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | | | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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10
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Yang Y, Wang C, Wei N, Hong T, Sun Z, Xiao J, Yao J, Li Z, Liu T. Identification of prognostic chromatin-remodeling genes in clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12:25614-25642. [PMID: 33232269 PMCID: PMC7803503 DOI: 10.18632/aging.104170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022]
Abstract
The aim of this study was to investigate the effects of chromatin-remodeling genes on the prognosis of patients with clear cell renal cell carcinoma (ccRCC). In TCGA-KIRC patients, two subgroups based on 86 chromatin-remodeling genes were established. The random forest algorithm was used for feature selection to identify BPTF, SIN3A and CNOT1 as characterized chromatin remodelers in ccRCC with good prognostic value. YY1 was indicated to be a transcription factor of genes highly related to BPTF, SIN3A and CNOT1. Functional annotations indicated that BPTF, SIN3A, CNOT1 and YY1 are all involved in the ubiquitin-mediated proteolysis process and that high expression of any of the five associated E3 ubiquitin ligases found in the pathway suggests a good prognosis. Protein network analysis indicated that BPTF has a targeted regulatory effect on YY1. Another independent dataset from International Cancer Genome Consortium (ICGC) showed a strong consistency with results in TCGA. In conclusion, we demonstrate that BPTF, SIN3A and CNOT1 are novel prognostic factors that predict good survival in ccRCC. We predicted that the good prognostic value of chromatin-remodeling genes BPTF and SIN3A is related to the regulation of YY1 and that YY1 regulates E3 ubiquitin ligases for further degradation of oncoproteins in ccRCC.
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Affiliation(s)
- Yujing Yang
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Chengyuan Wang
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Ningde Wei
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Ting Hong
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Zuyu Sun
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Jiawen Xiao
- Department of Medical Oncology, Shenyang Fifth People Hospital, Tiexi District, Shenyang 110001, P.R. China
| | - Jiaxi Yao
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Zhi Li
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Tao Liu
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
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11
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Sun G, Wang C, Wang S, Sun H, Zeng K, Zou R, Lin L, Liu W, Sun N, Song H, Liu W, Zhou T, Jin F, Shan Z, Zhao Y. An H3K4me3 reader, BAP18 as an adaptor of COMPASS-like core subunits co-activates ERα action and associates with the sensitivity of antiestrogen in breast cancer. Nucleic Acids Res 2020; 48:10768-10784. [PMID: 32986841 PMCID: PMC7641737 DOI: 10.1093/nar/gkaa787] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 08/19/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022] Open
Abstract
Estrogen receptor alpha (ERα) signaling pathway is essential for ERα-positive breast cancer progression and endocrine therapy resistance. Bromodomain PHD Finger Transcription Factor (BPTF) associated protein of 18kDa (BAP18) has been recognized as a crucial H3K4me3 reader. However, the whole genomic occupation of BAP18 and its biological function in breast cancer is still elusive. Here, we found that higher expression of BAP18 in ERα-positive breast cancer is positively correlated with poor prognosis. ChIP-seq analysis further demonstrated that the half estrogen response elements (EREs) and the CCCTC binding factor (CTCF) binding sites are the significant enrichment sites found in estrogen-induced BAP18 binding sites. Also, we provide the evidence to demonstrate that BAP18 as a novel co-activator of ERα is required for the recruitment of COMPASS-like core subunits to the cis-regulatory element of ERα target genes in breast cancer cells. BAP18 is recruited to the promoter regions of estrogen-induced genes, accompanied with the enrichment of the lysine 4-trimethylated histone H3 tail (H3K4me3) in the presence of E2. Furthermore, BAP18 promotes cell growth and associates the sensitivity of antiestrogen in ERα-positive breast cancer. Our data suggest that BAP18 facilitates the association between ERα and COMPASS-like core subunits, which might be an essential epigenetic therapeutic target for breast cancer.
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Affiliation(s)
- Ge Sun
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Chunyu Wang
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Shengli Wang
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Hongmiao Sun
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Kai Zeng
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Renlong Zou
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Lin Lin
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Wei Liu
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Ning Sun
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Huijuan Song
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Wensu Liu
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Tingting Zhou
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Feng Jin
- Department of Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang City 110001, Liaoning Province, China
| | - Zhongyan Shan
- Department of Endocrinology and Metabolism, Institute of Endocrinology, The First Affiliated Hospital of China Medical University, ShenyangCity110001, Liaoning Province, China
| | - Yue Zhao
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China.,Department of Endocrinology and Metabolism, Institute of Endocrinology, The First Affiliated Hospital of China Medical University, ShenyangCity110001, Liaoning Province, China
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12
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Miao J, Zhang M, Huang X, Xu L, Tang R, Wang H, Han S. Upregulation of bromodomain PHD finger transcription factor in ovarian cancer and its critical role for cancer cell proliferation and survival. Biochem Cell Biol 2020; 99:304-312. [PMID: 32985220 DOI: 10.1139/bcb-2020-0227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bromodomain PHD finger transcription factor (BPTF) is a core subunit of the nucleosome-remodeling factor (NURF) complex, which plays an important role in the development of several cancers. However, it is unknown whether BPTF regulates the progression of ovarian cancer (OC). To investigate this, we measured the relative expression levels of BPTF in OC cell lines and tissues using Western blot and immunohistochemistry, respectively, and the results were analyzed using the χ2 test. We also examined the effects from BPTF knockdown on the proliferation, migration, invasiveness, and apoptosis of OC cell lines. Mechanistic studies revealed that these effects were achieved through simultaneous modulation of multiple signaling pathways. We found that BPTF was highly expressed in OC cell lines and tissues compared with a normal human ovarian epithelial cell line and non-cancerous tissues (P < 0.05). These results are also supported by the public RNA-seq data. BPTF overexpression was correlated with a poor prognosis for OC patient survival (P < 0.05). In vitro experiments revealed that the downregulation of BPTF inhibited OC cell proliferation, colony formation, migration, and invasiveness, and induced apoptosis. BPTF knockdown also affected the epithelial-mesenchymal transition (EMT) signaling pathways and induced the cleavage of apoptosis-related proteins. Consequently, BPTF plays a critical role in OC cell survival, and functions as a potential therapeutic target for OC.
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Affiliation(s)
- Juan Miao
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Min Zhang
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 210004, China
| | - Xiaohao Huang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lei Xu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ranran Tang
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 210004, China
| | - Huan Wang
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 210004, China
| | - Suping Han
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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13
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ATP-Dependent Chromatin Remodeling Complex in the Lineage Specification of Mesenchymal Stem Cells. Stem Cells Int 2020; 2020:8839703. [PMID: 32963551 PMCID: PMC7499328 DOI: 10.1155/2020/8839703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal stem cells (MSCs) present in multiple tissues can self-renew and differentiate into multiple lineages including the bone, cartilage, muscle, cardiac tissue, and connective tissue. Key events, including cell proliferation, lineage commitment, and MSC differentiation, are ensured by precise gene expression regulation. ATP-dependent chromatin alteration is one form of epigenetic modifications that can regulate the transcriptional level of specific genes by utilizing the energy from ATP hydrolysis to reorganize chromatin structure. ATP-dependent chromatin remodeling complexes consist of a variety of subunits that together perform multiple functions in self-renewal and lineage specification. This review highlights the important role of ATP-dependent chromatin remodeling complexes and their different subunits in modulating MSC fate determination and discusses the proposed mechanisms by which ATP-dependent chromatin remodelers function.
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14
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Richart L, Felipe I, Delgado P, Andrés MPD, Prieto J, Pozo ND, García JF, Piris MA, Ramiro A, Real FX. Bptf determines oncogenic addiction in aggressive B-cell lymphomas. Oncogene 2020; 39:4884-4895. [PMID: 32451433 DOI: 10.1038/s41388-020-1331-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022]
Abstract
Chromatin remodeling factors contribute to establish aberrant gene expression programs in cancer cells and therefore represent valuable targets for therapeutic intervention. BPTF (Bromodomain PhD Transcription Factor), a core subunit of the nucleosome remodeling factor (NURF), modulates c-MYC oncogenic activity in pancreatic cancer. Here, we analyze the role of BPTF in c-MYC-driven B-cell lymphomagenesis using the Eμ-Myc transgenic mouse model of aggressive B-cell lymphoma. We find that BPTF is required for normal B-cell differentiation without evidence of haploinsufficiency. In contrast, deletion of one Bptf allele is sufficient to delay lymphomagenesis in Eμ-Myc mice. Tumors arising in a Bptf heterozygous background display decreased c-MYC levels and pathway activity, together with increased activation of the NF-κB pathway, a molecular signature characteristic of human diffuse large B-cell lymphoma (DLBCL). In human B-cell lymphoma samples, we find a strong correlation between BPTF and c-MYC mRNA and protein levels, together with an anti-correlation between BPTF and NF-κB pathway activity. Our results indicate that BPTF is a relevant therapeutic target in B-cell lymphomas and that, upon its inhibition, cells acquire distinct oncogenic dependencies.
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Affiliation(s)
- Laia Richart
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
| | - Irene Felipe
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
| | - Pilar Delgado
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | - Mónica P de Andrés
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
| | - Jaime Prieto
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
| | - Natalia Del Pozo
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Juan F García
- Department of Pathology, MD Anderson Cancer Center, 28033, Madrid, Spain
| | - Miguel A Piris
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Department of Pathology, Fundación Jiménez Díaz, 28040, Madrid, Spain.,Department of Pathology, Hospital Universitario Marqués de Valdecilla, 39008, Santander, Spain
| | - Almudena Ramiro
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain. .,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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15
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Olson NM, Kroc S, Johnson JA, Zahid H, Ycas PD, Chan A, Kimbrough JR, Kalra P, Schönbrunn E, Pomerantz WCK. NMR Analyses of Acetylated H2A.Z Isoforms Identify Differential Binding Interactions with the Bromodomain of the NURF Nucleosome Remodeling Complex. Biochemistry 2020; 59:1871-1880. [PMID: 32356653 DOI: 10.1021/acs.biochem.0c00159] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gene specific recruitment of bromodomain-containing proteins to chromatin is affected by post-translational acetylation of lysine on histones. Whereas interactions of the bromodomain with acetylation patterns of native histones (H2A, H2B, H3, and H4) have been well characterized, the motif for recognition for histone variants H2A.Z I and H2A.Z II by bromodomains has yet to be fully investigated. Elucidating these molecular mechanisms is crucial for understanding transcriptional regulation in cellular processes involved in both development and disease. Here, we have used protein-observed fluorine NMR to fully characterize the affinities of H2A.Z I and II acetylation patterns for BPTF's bromodomain and found the diacetylated mark of lysine 7 and 13 on H2A.Z II to have the strongest interaction with K7ac preferentially engaging the binding site. We further examined the selectivity of H2A.Z histones against a variety of bromodomains, revealing that the bromodomain of CECR2 binds with the highest affinity and specificity for acetylated H2A.Z I over isoform II. These results support a possible role for different H2A.Z transcriptional activation mechanisms that involve recruitment of chromatin remodeling complexes.
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Affiliation(s)
- Noelle M Olson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Samantha Kroc
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Jorden A Johnson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Peter D Ycas
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Alice Chan
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Jennifer R Kimbrough
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Prakriti Kalra
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
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16
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Xu W, Long L, Zhao Y, Stevens L, Felipe I, Munoz J, Ellis RE, McGrath PT. Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes. eLife 2019; 8:e48119. [PMID: 31498079 PMCID: PMC6752949 DOI: 10.7554/elife.48119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Genes can encode multiple isoforms, broadening their functions and providing a molecular substrate to evolve phenotypic diversity. Evolution of isoform function is a potential route to adapt to new environments. Here we show that de novo, beneficial alleles in the nurf-1 gene became fixed in two laboratory lineages of C. elegans after isolation from the wild in 1951, before methods of cryopreservation were developed. nurf-1 encodes an ortholog of BPTF, a large (>300 kD) multidomain subunit of the NURF chromatin remodeling complex. Using CRISPR-Cas9 genome editing and transgenic rescue, we demonstrate that in C. elegans, nurf-1 has split into two, largely non-overlapping isoforms (NURF-1.D and NURF-1.B, which we call Yin and Yang, respectively) that share only two of 26 exons. Both isoforms are essential for normal gametogenesis but have opposite effects on male/female gamete differentiation. Reproduction in hermaphrodites, which involves production of both sperm and oocytes, requires a balance of these opposing Yin and Yang isoforms. Transgenic rescue and genetic position of the fixed mutations suggest that different isoforms are modified in each laboratory strain. In a related clade of Caenorhabditis nematodes, the shared exons have duplicated, resulting in the split of the Yin and Yang isoforms into separate genes, each containing approximately 200 amino acids of duplicated sequence that has undergone accelerated protein evolution following the duplication. Associated with this duplication event is the loss of two additional nurf-1 transcripts, including the long-form transcript and a newly identified, highly expressed transcript encoded by the duplicated exons. We propose these lost transcripts are non-functional side products necessary to transcribe the Yin and Yang transcripts in the same cells. Our work demonstrates how gene sharing, through the production of multiple isoforms, can precede the creation of new, independent genes.
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Affiliation(s)
- Wen Xu
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Lijiang Long
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
- Interdisciplinary Graduate Program in Quantitative BiosciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Yuehui Zhao
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Irene Felipe
- Epithelial Carcinogenesis GroupSpanish National Cancer Research Center-CNIOMadridSpain
| | - Javier Munoz
- Proteomics Unit-ProteoRed-ISCIIISpanish National Cancer Research Center-CNIOMadridSpain
| | - Ronald E Ellis
- Department of Molecular BiologyRowan University School of Osteopathic MedicineStratfordUnited States
| | - Patrick T McGrath
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
- Parker H. Petit Institute of Bioengineering and BioscienceGeorgia Institute of TechnologyAtlantaUnited States
- School of PhysicsGeorgia Institute of TechnologyAtlantaUnited States
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17
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Xu J, Wang Q, Leung ELH, Li Y, Fan X, Wu Q, Yao X, Liu L. Compound C620-0696, a new potent inhibitor targeting BPTF, the chromatin-remodeling factor in non-small-cell lung cancer. Front Med 2019; 14:60-67. [PMID: 31104301 DOI: 10.1007/s11684-019-0694-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
Bromodomain PHD-finger transcription factor (BPTF) is the largest subunit of the nucleosome remodeling factor and plays an important role in chromatin remodeling for gene activation through its association with histone acetylation or methylation. BPTF is also involved in oncogene transcription in diverse progressions of cancers. Despite clinical trials for inhibitors of bromodomain and extra-terminal family proteins in human cancers, no potent and selective inhibitor targeting the BPTF bromodomain has been discovered. In this study, we identified a potential inhibitor, namely, C620-0696, by computational docking modeling to target bromodomain. Results of biolayer interferometry revealed that compound C620-0696 exhibited high binding affinity to the BPTF bromodomain. Moreover, C620-0696 was cytotoxic in BPTF with a high expression of non-small-cell lung cancer (NSCLC) cells. It suppressed the expression of the BPTF target gene c-MYC, which is known as an oncogenic transcriptional regulator in various cancers. C620-0696 also partially inhibited the migration and colony formation of NSCLC cells owing to apoptosis induction and cell cycle blockage. Thus, our study presents an effective strategy to target a bromodomain factor-mediated tumorigenesis in cancers with small molecules, supporting further exploration of the use of these inhibitors in oncology.
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Affiliation(s)
- Jiahui Xu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 519020, China
| | - Qianqian Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 519020, China
| | - Elaine Lai Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 519020, China
- Respiratory Medicine Department, Taihe Hospital, Hubei University of Medicine, Shiyan, 236600, China
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Health and State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Ying Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 519020, China
| | - Xingxing Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 519020, China
| | - Qibiao Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 519020, China.
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 519020, China.
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 519020, China.
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18
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Laurette P, Coassolo S, Davidson G, Michel I, Gambi G, Yao W, Sohier P, Li M, Mengus G, Larue L, Davidson I. Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma. Cell Death Differ 2019; 27:29-43. [PMID: 31065107 DOI: 10.1038/s41418-019-0333-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 03/04/2019] [Accepted: 03/28/2019] [Indexed: 11/09/2022] Open
Abstract
Somatic oncogenic mutation of BRAF coupled with inactivation of PTEN constitute a frequent combination of genomic alterations driving the development of human melanoma. Mice genetically engineered to conditionally express oncogenic BrafV600E and inactivate Pten in melanocytes following tamoxifen treatment rapidly develop melanoma. While early-stage melanomas comprised melanin-pigmented Mitf and Dct-expressing cells, expression of these and other melanocyte identity genes was lost in later stage tumours that showed histological and molecular characteristics of de-differentiated neural crest type cells. Melanocyte identity genes displayed loss of active chromatin marks and RNA polymerase II and gain of heterochromatin marks, indicating epigenetic reprogramming during tumour progression. Nevertheless, late-stage tumour cells grown in culture re-expressed Mitf, and melanocyte markers and Mitf together with Sox10 coregulated a large number of genes essential for their growth. In this melanoma model, somatic inactivation that the catalytic Brg1 (Smarca4) subunit of the SWI/SNF complex and the scaffolding Bptf subunit of the NuRF complex delayed tumour formation and deregulated large and overlapping gene expression programs essential for normal tumour cell growth. Moreover, we show that Brg1 and Bptf coregulated many genes together with Mitf and Sox10. Together these transcription factors and chromatin remodelling complexes orchestrate essential gene expression programs in mouse melanoma cells.
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Affiliation(s)
- Patrick Laurette
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Sébastien Coassolo
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Guillaume Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Isabelle Michel
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Giovanni Gambi
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Wenjin Yao
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Pierre Sohier
- INSERM U1021, Normal and Pathological Development of Melanocytes, Institut Curie, PSL Research University, Orsay, France.,Univ. Paris-Sud, Univ. Paris-Saclay, CNRS UMR3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Mei Li
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Lionel Larue
- INSERM U1021, Normal and Pathological Development of Melanocytes, Institut Curie, PSL Research University, Orsay, France.,Univ. Paris-Sud, Univ. Paris-Saclay, CNRS UMR3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France. .,Equipes Labellisées Ligue Contre le Cancer, Paris, France.
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19
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Jung YS, Kim MJ, Park JI. LncGata6-controlled stemness in regeneration and cancer. NON-CODING RNA INVESTIGATION 2019; 3:4. [PMID: 30775691 PMCID: PMC6377203 DOI: 10.21037/ncri.2019.01.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Youn-Sang Jung
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston,
TX, USA
| | - Moon Jong Kim
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston,
TX, USA
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston,
TX, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX,
USA
- Graduate School of Biomedical Sciences at Houston, The University of Texas MD Anderson Cancer Center and
Health Science Center, Houston, TX, USA
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20
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Zhao X, Zheng F, Li Y, Hao J, Tang Z, Tian C, Yang Q, Zhu T, Diao C, Zhang C, Chen M, Hu S, Guo P, Zhang L, Liao Y, Yu W, Chen M, Zou L, Guo W, Deng W. BPTF promotes hepatocellular carcinoma growth by modulating hTERT signaling and cancer stem cell traits. Redox Biol 2018; 20:427-441. [PMID: 30419422 PMCID: PMC6230923 DOI: 10.1016/j.redox.2018.10.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/21/2022] Open
Abstract
Bromodomain PHD finger transcription factor (BPTF), a core subunit of nucleosome-remodeling factor (NURF) complex, plays an important role in chromatin remodeling. However, its precise function and molecular mechanism involved in hepatocellular carcinoma (HCC) growth are still poorly defined. Here, we demonstrated the tumor-promoting role of BPTF in HCC progression. BPTF was highly expressed in HCC cells and tumor tissues of HCC patients compared with normal liver cells and tissues. Knockdown of BPTF inhibited cell proliferation, colony formation and stem cell-like traits in HCC cells. In addition, BPTF knockdown effectively sensitized the anti-tumor effect of chemotherapeutic drugs and induced more apoptosis in HCC cells. Consistently, knockdown of BPTF in a xenograft mouse model also suppressed tumor growth and metastasis accompanied by the suppression of cancer stem cells (CSC)-related protein markers. Moreover, the mechanism study showed that the tumor-promoting role of BPTF in HCC was realized by transcriptionally regulating the expression of human telomerase reverse transcriptase (hTERT). Furthermore, we found that HCC patients with high BPTF expression displayed high hTERT expression, and high BPTF or hTERT expression level was positively correlated with advanced malignancy and poor prognosis in HCC patients. Collectively, our results demonstrate that BPTF promotes HCC growth by targeting hTERT and suggest that the BPTF-hTERT axis maybe a novel and potential therapeutic target in HCC.
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Affiliation(s)
- Xinrui Zhao
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Fufu Zheng
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yizhuo Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Jiaojiao Hao
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Zhipeng Tang
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Chunfang Tian
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Qian Yang
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Tianhua Zhu
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Chaoliang Diao
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Changlin Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Manyu Chen
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Sheng Hu
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Ping Guo
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Lizhi Zhang
- The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Yina Liao
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Wendan Yu
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Miao Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Lijuan Zou
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Wei Guo
- Institute of Cancer Stem Cell & The Second Affiliated Hospital, Dalian Medical University, Dalian, China.
| | - Wuguo Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China.
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21
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The transcription factor Zfp90 regulates the self-renewal and differentiation of hematopoietic stem cells. Cell Death Dis 2018; 9:677. [PMID: 29880802 PMCID: PMC5992204 DOI: 10.1038/s41419-018-0721-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 12/21/2022]
Abstract
Hematopoietic stem cells (HSCs) can give rise to all blood cells that are essential to defend against pathogen invasion. The defective capability of HSC self-renewal is linked to many serious diseases, such as anemia. However, the potential mechanism regulating HSC self-renewal has not been thoroughly elucidated to date. In this study, we showed that Zfp90 was highly expressed in HSCs. Zfp90 deficiency in the hematopoietic system caused impaired HSPC pools and led to HSC dysfunction. We showed that Zfp90 deletion inhibited HSC proliferation, while HSC apoptosis was not affected. Regarding the mechanism of this effect on HSC proliferation, we found that Zfp90 interacted with Snf2l, a subunit of the NURF complex, to regulate Hoxa9 expression. Ectopic expression of Hoxa9 rescued the HSC repopulation capacity in Zfp90-deficient mice, which indicates that Hoxa9 is the downstream effector of Zfp90. In summary, our findings identify Zfp90 as a key transcription factor in determining the fate of HSCs.
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22
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Duan C, Wang H, Chen Y, Chu P, Xing T, Gao C, Yue Z, Zheng J, Jin M, Gu W, Ma X. Whole exome sequencing reveals novel somatic alterations in neuroblastoma patients with chemotherapy. Cancer Cell Int 2018; 18:21. [PMID: 29467591 PMCID: PMC5816515 DOI: 10.1186/s12935-018-0521-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 02/12/2018] [Indexed: 12/19/2022] Open
Abstract
Background We ought to explore the acquired somatic alterations, shedding light on genetic basis of somatic alterations in NB patients with chemotherapy. Methods Marrow blood samples from NB patients were collected before treatment, after the 2nd and 4th chemotherapy for baseline research and continuous monitoring by whole exome sequencing. Plasma cell free DNA (cfDNA) was prepared for baseline research. Finger nail cells were extracted as self control. The clinical data was analyzed. Results From December 2014 to February 2016, 27 cases of children with stage IV NB were diagnosed. The follow up time ranged from 5 to 25 months, with a median follow up time of 17 months, 20 patients were stable, one patient died of pulmonary embolism during surgery, six patients died of disease progression. Marrow blood whole exome sequencing demonstrated that several novel somatic mutations were identified in all three trios comply or against the trendy of tumor size variation. Of note, six recurrent mutations in bromodomain PHD finger transcription factor (BPTF) were identified in nine NB patients under the continuous monitoring. The mutation rates variation was positively correlated to tumor size (CC = 0.428, P = 0.021), and patients with BPTF mutation may have a worse prognosis compared with wild type. Meanwhile, CGREF1, CUX2, GP1BA, SLC45A1 and TRA2A were mutated with the trendy oppose as therapeutic effects. The baseline research in three NB patients demonstrated that mutation rate of BPTF, TMCO3, GPRIN2 and C20orf96 in plasma cfDNA were in positive correlation with bone marrow genomic DNA (P = 0.001). Conclusions Our study showed that BPTF along with other mutations may function as a biomarker for evaluating to effects of chemotherapy to this refractory tumor, and patients with BPTF mutation might have a worse prognosis. Electronic supplementary material The online version of this article (10.1186/s12935-018-0521-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Duan
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Han Wang
- Joy Orient Translational Medicine Research Center for the Sequences Analysis and Blast, Beijing, China
| | - Ying Chen
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Ping Chu
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Tianyu Xing
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Chao Gao
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Zhixia Yue
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Jie Zheng
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Mei Jin
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Weiyue Gu
- Joy Orient Translational Medicine Research Center for the Sequences Analysis and Blast, Beijing, China
| | - Xiaoli Ma
- 1Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nanlishi Road, Beijing, 100045 China
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23
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Xu B, Cai L, Butler JM, Chen D, Lu X, Allison DF, Lu R, Rafii S, Parker JS, Zheng D, Wang GG. The Chromatin Remodeler BPTF Activates a Stemness Gene-Expression Program Essential for the Maintenance of Adult Hematopoietic Stem Cells. Stem Cell Reports 2018; 10:675-683. [PMID: 29456179 PMCID: PMC5918338 DOI: 10.1016/j.stemcr.2018.01.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 12/16/2022] Open
Abstract
Self-renewal and differentiation of adult stem cells are tightly regulated partly through configuration of chromatin structure by chromatin remodelers. Using knockout mice, we here demonstrate that bromodomain PHD finger transcription factor (BPTF), a component of the nucleosome remodeling factor (NURF) chromatin-remodeling complex, is essential for maintaining the population size of hematopoietic stem/progenitor cells (HSPCs), including long-term hematopoietic stem cells (HSCs). Bptf-deficient HSCs are defective in reconstituted hematopoiesis, and hematopoietic-specific knockout of Bptf caused profound defects including bone marrow failure and anemia. Genome-wide transcriptome profiling revealed that BPTF loss caused downregulation of HSC-specific gene-expression programs, which contain several master transcription factors (Meis1, Pbx1, Mn1, and Lmo2) required for HSC maintenance and self-renewal. Furthermore, we show that BPTF potentiates the chromatin accessibility of key HSC “stemness” genes. These results demonstrate an essential requirement of the chromatin remodeler BPTF and NURF for activation of “stemness” gene-expression programs and proper function of adult HSCs. The chromatin remodeler gene Bptf shows preferential expression in primitive HSPCs Bptf ensures maintenance and functionality of HSCs in a cell-autonomous manner Bptf is required for the activation of HSC “stemness” genes including master TFs Hematopoietic-specific loss of Bptf results in bone marrow failure and anemia
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Affiliation(s)
- Bowen Xu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason M Butler
- Department of Medicine and Ansary Stem Cell Institute, Weill Cornell Medical College, New York, NY 10065, USA
| | - Dongliang Chen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Xiongdong Lu
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - David F Allison
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Rui Lu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Shahin Rafii
- Department of Medicine and Ansary Stem Cell Institute, Weill Cornell Medical College, New York, NY 10065, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Deyou Zheng
- Department of Neuroscience and Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
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24
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Goodwin LR, Picketts DJ. The role of ISWI chromatin remodeling complexes in brain development and neurodevelopmental disorders. Mol Cell Neurosci 2017; 87:55-64. [PMID: 29249292 DOI: 10.1016/j.mcn.2017.10.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/04/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022] Open
Abstract
The mammalian ISWI (Imitation Switch) genes SMARCA1 and SMARCA5 encode the ATP-dependent chromatin remodeling proteins SNF2L and SNF2H. The ISWI proteins interact with BAZ (bromodomain adjacent to PHD zinc finger) domain containing proteins to generate eight distinct remodeling complexes. ISWI complex-mediated nucleosome positioning within genes and gene regulatory elements is proving important for the transition from a committed progenitor state to a differentiated cell state. Genetic studies have implicated the involvement of many ATP-dependent chromatin remodeling proteins in neurodevelopmental disorders (NDDs), including SMARCA1. Here we review the characterization of mice inactivated for ISWI and their interacting proteins, as it pertains to brain development and disease. A better understanding of chromatin dynamics during neural development is a prerequisite to understanding disease pathologies and the development of therapeutics for these complex disorders.
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Affiliation(s)
- Laura R Goodwin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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25
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Hota SK, Bruneau BG. ATP-dependent chromatin remodeling during mammalian development. Development 2017; 143:2882-97. [PMID: 27531948 DOI: 10.1242/dev.128892] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise gene expression ensures proper stem and progenitor cell differentiation, lineage commitment and organogenesis during mammalian development. ATP-dependent chromatin-remodeling complexes utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression. These complexes contain diverse subunits that together provide a multitude of functions, from early embryogenesis through cell differentiation and development into various adult tissues. Here, we review the functions of chromatin remodelers and their different subunits during mammalian development. We discuss the mechanisms by which chromatin remodelers function and highlight their specificities during mammalian cell differentiation and organogenesis.
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Affiliation(s)
- Swetansu K Hota
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Department of Pediatrics, University of California, San Francisco, CA 94143, USA Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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26
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Perell GT, Mishra NK, Sudhamalla B, Ycas PD, Islam K, Pomerantz WCK. Specific Acetylation Patterns of H2A.Z Form Transient Interactions with the BPTF Bromodomain. Biochemistry 2017; 56:4607-4615. [PMID: 28771339 PMCID: PMC5779092 DOI: 10.1021/acs.biochem.7b00648] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational lysine acetylation of histone tails affects both chromatin accessibility and recruitment of multifunctional bromodomain-containing proteins for modulating transcription. The bromodomain- and PHD finger-containing transcription factor (BPTF) regulates transcription but has also been implicated in high gene expression levels in a variety of cancers. In this report, the histone variant H2A.Z, which replaces H2A in chromatin, is evaluated for its affinity for BPTF with a specific recognition pattern of acetylated lysine residues of the N-terminal tail region. Although BPTF immunoprecipitates H2A.Z-containing nucleosomes, a direct interaction with its bromodomain has not been reported. Using protein-observed fluorine nuclear magnetic resonance (PrOF NMR) spectroscopy, we identified a diacetylation of H2A.Z on lysine residues 4 and 11, with the highest affinity for BPTF with a Kd of 780 μM. A combination of subsequent 1H NMR Carr-Purcell-Meiboom-Gill experiments and photo-cross-linking further confirmed the specificity of the diacetylation pattern at lysines 4 and 11. Because of an adjacent PHD domain, this transient interaction may contribute to a higher-affinity bivalent interaction. Further evaluation of specificity toward a set of bromodomains, including two BET bromodomains (Brd4 and BrdT) and two Plasmodium falciparum bromodomains, resulted in one midmicromolar affinity binder, PfGCN5 (Kd = 650 μM). With these biochemical experiments, we have identified a direct interaction of histone H2A.Z with bromodomains with a specific acetylation pattern that further supports the role of H2A.Z in epigenetic regulation.
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Affiliation(s)
- Gabriella T. Perell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Neeraj K. Mishra
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Babu Sudhamalla
- Department of Chemistry, University of Pittsburgh, 1307 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Peter D. Ycas
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, 1307 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
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27
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Oppikofer M, Bai T, Gan Y, Haley B, Liu P, Sandoval W, Ciferri C, Cochran AG. Expansion of the ISWI chromatin remodeler family with new active complexes. EMBO Rep 2017; 18:1697-1706. [PMID: 28801535 DOI: 10.15252/embr.201744011] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
ISWI chromatin remodelers mobilize nucleosomes to control DNA accessibility. Complexes isolated to date pair one of six regulatory subunits with one of two highly similar ATPases. However, we find that each endogenously expressed ATPase co-purifies with every regulatory subunit, substantially increasing the diversity of ISWI complexes, and we additionally identify BAZ2B as a novel, seventh regulatory subunit. Through reconstitution of catalytically active human ISWI complexes, we demonstrate that the new interactions described here are stable and direct. Finally, we profile the nucleosome remodeling functions of the now expanded family of ISWI chromatin remodelers. By revealing the combinatorial nature of ISWI complexes, we provide a basis for better understanding ISWI function in normal settings and disease.
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Affiliation(s)
- Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Tianyi Bai
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Yutian Gan
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Liu
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
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28
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Frey WD, Chaudhry A, Slepicka PF, Ouellette AM, Kirberger SE, Pomerantz WCK, Hannon GJ, Dos Santos CO. BPTF Maintains Chromatin Accessibility and the Self-Renewal Capacity of Mammary Gland Stem Cells. Stem Cell Reports 2017; 9:23-31. [PMID: 28579392 PMCID: PMC5783326 DOI: 10.1016/j.stemcr.2017.04.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 11/16/2022] Open
Abstract
Chromatin remodeling is a key requirement for transcriptional control of cellular differentiation. However, the factors that alter chromatin architecture in mammary stem cells (MaSCs) are poorly understood. Here, we show that BPTF, the largest subunit of the NURF chromatin remodeling complex, is essential for MaSC self-renewal and differentiation of mammary epithelial cells (MECs). BPTF depletion arrests cells at a previously undefined stage of epithelial differentiation that is associated with an incapacity to achieve the luminal cell fate. Moreover, genome-wide analysis of DNA accessibility following genetic or chemical inhibition, suggests a role for BPTF in maintaining the open chromatin landscape at enhancers regions in MECs. Collectively, our study implicates BPTF in maintaining the unique epigenetic state of MaSCs.
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Affiliation(s)
- Wesley D Frey
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Anisha Chaudhry
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Priscila F Slepicka
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Adam M Ouellette
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Steven E Kirberger
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, MN 55455, USA
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, MN 55455, USA
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB20RE, UK.
| | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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29
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Wu B, Wang Y, Wang C, Wang GG, Wu J, Wan YY. BPTF Is Essential for T Cell Homeostasis and Function. THE JOURNAL OF IMMUNOLOGY 2016; 197:4325-4333. [PMID: 27799308 DOI: 10.4049/jimmunol.1600642] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/03/2016] [Indexed: 12/31/2022]
Abstract
Bromodomain PHD finger transcription factor (BPTF), a ubiquitously expressed ATP-dependent chromatin-remodeling factor, is critical for epigenetically regulating DNA accessibility and gene expression. Although BPTF is important for the development of thymocytes, its function in mature T cells remains largely unknown. By specifically deleting BPTF from late double-negative 3/double-negative 4 stage of developing T cells, we found that BPTF was critical for the homeostasis of T cells via a cell-intrinsic manner. In addition, BPTF was essential for the maintenance and function of regulatory T (Treg) cells. Treg cell-specific BPTF deletion led to reduced Foxp3 expression, increased lymphocyte infiltration in the nonlymphoid organs, and a systemic autoimmune syndrome. These findings therefore reveal a vital role for BPTF in T and Treg cell function and immune homeostasis.
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Affiliation(s)
- Bing Wu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Yunqi Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Chaojun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,State Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; and
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jie Wu
- State Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; and
| | - Yisong Y Wan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; .,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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30
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Mayes K, Alkhatib SG, Peterson K, Alhazmi A, Song C, Chan V, Blevins T, Roberts M, Dumur CI, Wang XY, Landry JW. BPTF Depletion Enhances T-cell-Mediated Antitumor Immunity. Cancer Res 2016; 76:6183-6192. [PMID: 27651309 DOI: 10.1158/0008-5472.can-15-3125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 08/24/2016] [Indexed: 12/12/2022]
Abstract
Genetic studies in fruit flies have implicated the chromatin remodeling complex nucleosome remodeling factor (NURF) in immunity, but it has yet to be studied in mammals. Here we show that its targeting in mice enhances antitumor immunity in two syngeneic models of cancer. NURF was disabled by silencing of bromodomain PHD-finger containing transcription factor (BPTF), the largest and essential subunit of NURF. We found that both CD8+ and CD4+ T cells were necessary for enhanced antitumor activity, with elevated numbers of activated CD8+ T cells observed in BPTF-deficient tumors. Enhanced cytolytic activity was observed for CD8+ T cells cocultured with BPTF-silenced cells. Similar effects were not produced with T-cell receptor transgenic CD8+ T cells, implicating the involvement of novel antigens. Accordingly, enhanced activity was observed for individual CD8+ T-cell clones from mice bearing BPTF-silenced tumors. Mechanistic investigations revealed that NURF directly regulated the expression of genes encoding immunoproteasome subunits Psmb8 and Psmb9 and the antigen transporter genes Tap1 and Tap2 The PSMB8 inhibitor ONX-0914 reversed the effects of BPTF ablation, consistent with a critical role for the immunoproteasome in improving tumor immunogenicity. Thus, NURF normally suppresses tumor antigenicity and its depletion improves antigen processing, CD8 T-cell cytotoxicity, and antitumor immunity, identifying NURF as a candidate therapeutic target to enhance antitumor immunity. Cancer Res; 76(21); 6183-92. ©2016 AACR.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Suehyb G Alkhatib
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Kristen Peterson
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Carolyn Song
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Vivian Chan
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Tana Blevins
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Mark Roberts
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Catherine I Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Xiang-Yang Wang
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Joseph W Landry
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia.
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31
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Large EE, Xu W, Zhao Y, Brady SC, Long L, Butcher RA, Andersen EC, McGrath PT. Selection on a Subunit of the NURF Chromatin Remodeler Modifies Life History Traits in a Domesticated Strain of Caenorhabditis elegans. PLoS Genet 2016; 12:e1006219. [PMID: 27467070 PMCID: PMC4965130 DOI: 10.1371/journal.pgen.1006219] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/01/2016] [Indexed: 11/20/2022] Open
Abstract
Evolutionary life history theory seeks to explain how reproductive and survival traits are shaped by selection through allocations of an individual’s resources to competing life functions. Although life-history traits evolve rapidly, little is known about the genetic and cellular mechanisms that control and couple these tradeoffs. Here, we find that two laboratory-adapted strains of C. elegans descended from a single common ancestor that lived in the 1950s have differences in a number of life-history traits, including reproductive timing, lifespan, dauer formation, growth rate, and offspring number. We identified a quantitative trait locus (QTL) of large effect that controls 24%–75% of the total trait variance in reproductive timing at various timepoints. Using CRISPR/Cas9-induced genome editing, we show this QTL is due in part to a 60 bp deletion in the 3’ end of the nurf-1 gene, which is orthologous to the human gene encoding the BPTF component of the NURF chromatin remodeling complex. Besides reproduction, nurf-1 also regulates growth rate, lifespan, and dauer formation. The fitness consequences of this deletion are environment specific—it increases fitness in the growth conditions where it was fixed but decreases fitness in alternative laboratory growth conditions. We propose that chromatin remodeling, acting through nurf-1, is a pleiotropic regulator of life history trade-offs underlying the evolution of multiple traits across different species. Sex and death are two fundamental concerns of each organism. These traits evolve rapidly in natural populations as animals seek to maximize their fitness in a given environment. For example, in mammals, lifespan, size, and fecundity vary over two order of magnitude. A key observation of evolutionary life history theory is the recognition that there are limited amount of resources available, which creates tradeoffs between competing life functions. By studying a domesticated strain of C. elegans, we identify a beneficial mutation that regulates a number of life history tradeoffs. This mutation affects a subunit of the NURF chromatin remodeling complex. Our work suggests that NURF is a master regulator of life history tradeoffs through epigenetic regulation, and a target of evolution.
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Affiliation(s)
- Edward E. Large
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Wen Xu
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Yuehui Zhao
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Shannon C. Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Lijiang Long
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Rebecca A. Butcher
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Patrick T. McGrath
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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32
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Hsu FC, Shapiro MJ, Dash B, Chen CC, Constans MM, Chung JY, Romero Arocha SR, Belmonte PJ, Chen MW, McWilliams DC, Shapiro VS. An Essential Role for the Transcription Factor Runx1 in T Cell Maturation. Sci Rep 2016; 6:23533. [PMID: 27020276 PMCID: PMC4810436 DOI: 10.1038/srep23533] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/08/2016] [Indexed: 12/26/2022] Open
Abstract
The transcription factor Runx1 has essential roles throughout hematopoiesis. Here, we demonstrate that Runx1 is critical for T cell maturation. Peripheral naïve CD4(+) T cells from CD4-cre Runx1 cKO mice are phenotypically and functionally immature as shown by decreased production of TNF-α upon TCR stimulation. The loss of peripheral CD4(+) T cells in CD4-cre Runx1 cKO mice is not due to defects in homeostasis or decreased expression of IL-7Rα, as transgenic expression of IL-7Rα does not rescue the loss of CD4(+) T cells. Rather, immature Runx1-deficient CD4(+) T cells are eliminated in the periphery by the activation and fixation of the classical complement pathway. In the thymus, there is a severe block in all aspects of intrathymic T cell maturation, although both positive and negative selection are unaltered. Thus, loss of Runx1 leads to the earliest characterized block in post-positive selection intrathymic maturation of CD4 T cells.
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Affiliation(s)
- Fan-Chi Hsu
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | | | - Barsha Dash
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Chien-Chang Chen
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Megan M Constans
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Ji Young Chung
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | | | - Paul J Belmonte
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Meibo W Chen
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
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Hogquist KA, Xing Y, Hsu FC, Shapiro VS. T Cell Adolescence: Maturation Events Beyond Positive Selection. THE JOURNAL OF IMMUNOLOGY 2015; 195:1351-7. [PMID: 26254267 DOI: 10.4049/jimmunol.1501050] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Single-positive thymocytes that successfully complete positive and negative selection must still undergo one final step, generally termed T cell maturation, before they gain functional competency and enter the long-lived T cell pool. Maturation initiates after positive selection in single-positive thymocytes and continues in the periphery in recent thymic emigrants, before these newly produced T cells gain functional competency and are ready to participate in the immune response as peripheral naive T cells. Recent work using genetically altered mice demonstrates that T cell maturation is not a single process, but a series of steps that occur independently and sequentially after positive selection. This review focuses on the changes that occur during T cell maturation, as well as the molecules and pathways that are critical at each step.
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Affiliation(s)
- Kristin A Hogquist
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; and
| | - Yan Xing
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; and
| | - Fan-Chi Hsu
- Department of Immunology, Mayo Clinic, Rochester, MN 55905
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34
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Dai M, Lu JJ, Guo W, Yu W, Wang Q, Tang R, Tang Z, Xiao Y, Li Z, Sun W, Sun X, Qin Y, Huang W, Deng WG, Wu T. BPTF promotes tumor growth and predicts poor prognosis in lung adenocarcinomas. Oncotarget 2015; 6:33878-92. [PMID: 26418899 PMCID: PMC4741809 DOI: 10.18632/oncotarget.5302] [Citation(s) in RCA: 39] [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: 03/12/2015] [Accepted: 09/11/2015] [Indexed: 01/07/2023] Open
Abstract
BPTF, a subunit of NURF, is well known to be involved in the development of eukaryotic cell, but little is known about its roles in cancers, especially in non-small-cell lung cancer (NSCLC). Here we showed that BPTF was specifically overexpressed in NSCLC cell lines and lung adenocarcinoma tissues. Knockdown of BPTF by siRNA significantly inhibited cell proliferation, induced cell apoptosis and arrested cell cycle progress from G1 to S phase. We also found that BPTF knockdown downregulated the expression of the phosphorylated Erk1/2, PI3K and Akt proteins and induced the cleavage of caspase-8, caspase-7 and PARP proteins, thereby inhibiting the MAPK and PI3K/AKT signaling and activating apoptotic pathway. BPTF knockdown by siRNA also upregulated the cell cycle inhibitors such as p21 and p18 but inhibited the expression of cyclin D, phospho-Rb and phospho-cdc2 in lung cancer cells. Moreover, BPTF knockdown by its specific shRNA inhibited lung cancer growth in vivo in the xenografts of A549 cells accompanied by the suppression of VEGF, p-Erk and p-Akt expression. Immunohistochemical assay for tumor tissue microarrays of lung tumor tissues showed that BPTF overexpression predicted a poor prognosis in the patients with lung adenocarcinomas. Therefore, our data indicate that BPTF plays an essential role in cell growth and survival by targeting multiply signaling pathways in human lung cancers.
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Affiliation(s)
- Meng Dai
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Jian-Jun Lu
- Department of Thoracic Surgery, The First Affiliated Hospital,Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Guo
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Wendan Yu
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Qimin Wang
- The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Ranran Tang
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Zhipeng Tang
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Yao Xiao
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Zhenglin Li
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Wei Sun
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Xiuna Sun
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Yu Qin
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
| | - Wenlin Huang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
- State Key Laboratory of Targeted Drug for Tumors of Guangdong Province, Guangzhou Double Bioproduct Inc., Guangzhou, China
| | - Wu-guo Deng
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
- State Key Laboratory of Targeted Drug for Tumors of Guangdong Province, Guangzhou Double Bioproduct Inc., Guangzhou, China
| | - Taihua Wu
- The First Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Central Hospital, Dalian Medical University, Dalian, China
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35
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Koludrovic D, Laurette P, Strub T, Keime C, Le Coz M, Coassolo S, Mengus G, Larue L, Davidson I. Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells. PLoS Genet 2015; 11:e1005555. [PMID: 26440048 PMCID: PMC4595011 DOI: 10.1371/journal.pgen.1005555] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/07/2015] [Indexed: 12/23/2022] Open
Abstract
MIcrophthalmia-associated Transcription Factor (MITF) regulates melanocyte and melanoma physiology. We show that MITF associates the NURF chromatin-remodelling factor in melanoma cells. ShRNA-mediated silencing of the NURF subunit BPTF revealed its essential role in several melanoma cell lines and in untransformed melanocytes in vitro. Comparative RNA-seq shows that MITF and BPTF co-regulate overlapping gene expression programs in cell lines in vitro. Somatic and specific inactivation of Bptf in developing murine melanoblasts in vivo shows that Bptf regulates their proliferation, migration and morphology. Once born, Bptf-mutant mice display premature greying where the second post-natal coat is white. This second coat is normally pigmented by differentiated melanocytes derived from the adult melanocyte stem cell (MSC) population that is stimulated to proliferate and differentiate at anagen. An MSC population is established and maintained throughout the life of the Bptf-mutant mice, but these MSCs are abnormal and at anagen, give rise to reduced numbers of transient amplifying cells (TACs) that do not express melanocyte markers and fail to differentiate into mature melanin producing melanocytes. MSCs display a transcriptionally repressed chromatin state and Bptf is essential for reactivation of the melanocyte gene expression program at anagen, the subsequent normal proliferation of TACs and their differentiation into mature melanocytes. The melanocytes pigmenting the coat of adult mice derive from the melanocyte stem cell population residing in the permanent bulge area of the hair follicle. At each angen phase, melanocyte stem cells are stimulated to generate proliferative transient amplifying cells that migrate to the bulb of the follicle where they differentiate into mature melanin producing melanocytes, a processes involving MIcrophthalmia-associated Transcription Factor (MITF) the master regulator of the melanocyte lineage. We show that MITF associates with the NURF chromatin-remodelling factor in melanoma cells. NURF acts downstream of MITF in melanocytes and melanoma cells co-regulating gene expression in vitro. In vivo, mice lacking the NURF subunit Bptf in the melanocyte lineage show premature greying as they are unable to generate mature melanocytes from the adult stem cell population. We find that the melanocyte stem cells from these animals are abnormal and that once they are stimulated at anagen, Bptf is required to ensure the expression of melanocyte markers and their differentiation into mature adult melanocytes. Chromatin remodelling by NURF therefore appears to be essential for the transition of the transcriptionally quiescent stem cell to the differentiated state.
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Affiliation(s)
- Dana Koludrovic
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
- Beaston Institute for Cancer Research, Glasgow, United Kingdom
| | - Patrick Laurette
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Thomas Strub
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Céline Keime
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Madeleine Le Coz
- Institut Curie CNRS UMR3347, INSERM U1021, Bat 110, Orsay, France
| | - Sebastien Coassolo
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Lionel Larue
- Institut Curie CNRS UMR3347, INSERM U1021, Bat 110, Orsay, France
- Equipes labélisées Ligue Contre le Cancer, Orsay and Strasbourg, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
- Equipes labélisées Ligue Contre le Cancer, Orsay and Strasbourg, France
- * E-mail:
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36
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Hsu FC, Belmonte PJ, Constans MM, Chen MW, McWilliams DC, Hiebert SW, Shapiro VS. Histone Deacetylase 3 Is Required for T Cell Maturation. THE JOURNAL OF IMMUNOLOGY 2015; 195:1578-90. [PMID: 26163592 DOI: 10.4049/jimmunol.1500435] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/16/2015] [Indexed: 12/26/2022]
Abstract
Recent thymic emigrants are newly generated T cells that need to undergo postthymic maturation to gain functional competency and enter the long-lived naive T cell pool. The mechanism of T cell maturation remains incompletely understood. Previously, we demonstrated that the transcriptional repressor NKAP is required for T cell maturation. Because NKAP associates with histone deacetylase 3 (HDAC3), we examined whether HDAC3 is also required for T cell maturation. Although thymic populations are similar in CD4-cre HDAC3 conditional knockout mice compared with wild-type mice, the peripheral numbers of CD4(+) and CD8(+) T cells are dramatically decreased. In the periphery, the majority of HDAC3-deficient naive T cells are recent thymic emigrants, indicating a block in T cell maturation. CD55 upregulation during T cell maturation is substantially decreased in HDAC3-deficient T cells. Consistent with a block in functional maturation, HDAC3-deficient peripheral T cells have a defect in TNF licensing after TCR/CD28 stimulation. CD4-cre HDAC3 conditional knockout mice do not have a defect in intrathymic migration, thymic egress, T cell survival, or homeostasis. In the periphery, similar to immature NKAP-deficient peripheral T cells, HDAC3-deficient peripheral T cells were bound by IgM and complement proteins, leading to the elimination of these cells. In addition, HDAC3-deficient T cells display decreases in the sialic acid modifications on the cell surface that recruit natural IgM to initiate the classical complement pathway. Therefore, HDAC3 is required for T cell maturation.
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Affiliation(s)
- Fan-Chi Hsu
- Department of Immunology, Mayo Clinic, Rochester, MN 55905; and
| | - Paul J Belmonte
- Department of Immunology, Mayo Clinic, Rochester, MN 55905; and
| | | | - Meibo W Chen
- Department of Immunology, Mayo Clinic, Rochester, MN 55905; and
| | | | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
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37
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Abstract
The multiple lineages and differentiation states that constitute the T-cell compartment all derive from a common thymic precursor. These distinct transcriptional states are maintained both in time and after multiple rounds of cell division by the concerted actions of a small set of lineage-defining transcription factors that act in conjunction with a suite of chromatin-modifying enzymes to activate, repress, and fine-tune gene expression. These chromatin modifications collectively provide an epigenetic code that allows the stable and heritable maintenance of the T-cell phenotype. Recently, it has become apparent that the epigenetic code represents a therapeutic target for a variety of immune cell disorders, including lymphoma and acute and chronic inflammatory diseases. Here, we review the recent advances in epigenetic regulation of gene expression, particularly as it relates to the T-cell differentiation and function.
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Affiliation(s)
- Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia; Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
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38
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Dar AA, Nosrati M, Bezrookove V, de Semir D, Majid S, Thummala S, Sun V, Tong S, Leong SPL, Minor D, Billings PR, Soroceanu L, Debs R, Miller JR, Sagebiel RW, Kashani-Sabet M. The role of BPTF in melanoma progression and in response to BRAF-targeted therapy. J Natl Cancer Inst 2015; 107:djv034. [PMID: 25713167 PMCID: PMC4555639 DOI: 10.1093/jnci/djv034] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background: Bromodomain PHD finger transcription factor (BPTF) plays an important role in chromatin remodeling, but its functional role in tumor progression is incompletely understood. Here we explore the oncogenic effects of BPTF in melanoma. Methods: The consequences of differential expression of BPTF were explored using shRNA-mediated knockdown in several melanoma cell lines. Immunoblotting was used to assess the expression of various proteins regulated by BPTF. The functional role of BPTF in melanoma progression was investigated using assays of colony formation, invasion, cell cycle, sensitivity to selective BRAF inhibitors, and in xenograft models of melanoma progression (n = 12 mice per group). The biomarker role of BPTF in melanoma progression was assessed using fluorescence in situ hybridization and immunohistochemical analyses. All statistical tests were two-sided. Results: shRNA-mediated BPTF silencing suppressed the proliferative capacity (by 65.5%) and metastatic potential (by 66.4%) of melanoma cells. Elevated BPTF copy number (mean ≥ 3) was observed in 28 of 77 (36.4%) melanomas. BPTF overexpression predicted poor survival in a cohort of 311 melanoma patients (distant metastasis-free survival P = .03, and disease-specific survival P = .008), and promoted resistance to BRAF inhibitors in melanoma cell lines. Metastatic melanoma tumors progressing on BRAF inhibitors contained low BPTF-expressing, apoptotic tumor cell subclones, indicating the continued presence of drug-responsive subclones within tumors demonstrating overall resistance to anti-BRAF agents. Conclusions: These studies demonstrate multiple protumorigenic functions for BPTF and identify it as a novel target for anticancer therapy. They also suggest the combination of BPTF targeting with BRAF inhibitors as a novel therapeutic strategy for melanomas with mutant BRAF.
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Affiliation(s)
- Altaf A Dar
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Mehdi Nosrati
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Vladimir Bezrookove
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - David de Semir
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Shahana Majid
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Suresh Thummala
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Vera Sun
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Schuyler Tong
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Stanley P L Leong
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - David Minor
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Paul R Billings
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Liliana Soroceanu
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Robert Debs
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - James R Miller
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Richard W Sagebiel
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB)
| | - Mohammed Kashani-Sabet
- Center for Melanoma Research and Treatment (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, JRMIII, RWS, MKS), California Pacific Medical Center Research Institute, San Francisco, CA (AAD, MN, VB, DdS, ST, VS, ST, SPLL, DM, LS, RD, JRMIII, RWS, MKS); Department of Urology, Veterans Affairs Medical Center and University of California San Francisco, San Francisco, CA (SM); Life Technologies, Inc. Carlsbad, CA (PRB).
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The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia. BIOMED RESEARCH INTERNATIONAL 2015; 2015:347571. [PMID: 25789315 PMCID: PMC4348595 DOI: 10.1155/2015/347571] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/27/2015] [Indexed: 12/15/2022]
Abstract
Here, we review the role of sucrose nonfermenting (SNF2) family enzymes in blood cell development. The SNF2 family comprises helicase-like ATPases, originally discovered in yeast, that can remodel chromatin by changing chromatin structure and composition. The human genome encodes 30 different SNF2 enzymes. SNF2 family enzymes are often part of multisubunit chromatin remodeling complexes (CRCs), which consist of noncatalytic/auxiliary subunit along with the ATPase subunit. However, blood cells express a limited set of SNF2 ATPases that are necessary to maintain the pool of hematopoietic stem cells (HSCs) and drive normal blood cell development and differentiation. The composition of CRCs can be altered by the association of specific auxiliary subunits. Several auxiliary CRC subunits have specific functions in hematopoiesis. Aberrant expressions of SNF2 ATPases and/or auxiliary CRC subunit(s) are often observed in hematological malignancies. Using large-scale data from the International Cancer Genome Consortium (ICGC) we observed frequent mutations in genes encoding SNF2 helicase-like enzymes and auxiliary CRC subunits in leukemia. Hence, orderly function of SNF2 family enzymes is crucial for the execution of normal blood cell developmental program, and defects in chromatin remodeling caused by mutations or aberrant expression of these proteins may contribute to leukemogenesis.
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Yu Z, Liu J, Deng WM, Jiao R. Histone chaperone CAF-1: essential roles in multi-cellular organism development. Cell Mol Life Sci 2015; 72:327-37. [PMID: 25292338 PMCID: PMC11114026 DOI: 10.1007/s00018-014-1748-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 09/16/2014] [Accepted: 09/29/2014] [Indexed: 01/01/2023]
Abstract
More and more studies have shown chromatin remodelers and histone modifiers play essential roles in regulating developmental patterns by organizing specific chromosomal architecture to establish programmed transcriptional profiles, with implications that histone chaperones execute a coordinating role in these processes. Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved three-subunit protein complex, was identified as a histone chaperone coupled with DNA replication and repair in cultured mammalian cells and yeasts. Interestingly, recent findings indicate CAF-1 may have important regulatory roles during development by interacting with specific transcription factors and epigenetic regulators. In this review, we focus on the essential roles of CAF-1 in regulating heterochromatin organization, asymmetric cell division, and specific signal transduction through epigenetic modulations of the chromatin. In the end, we aim at providing a current image of facets of CAF-1 as a histone chaperone to orchestrate cell proliferation and differentiation during multi-cellular organism development.
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Affiliation(s)
- Zhongsheng Yu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100080 China
| | - Jiyong Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- Guangzhou Hoffmann Institute of Immunology, School of Basic Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou, 510182 China
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295 USA
| | - Renjie Jiao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100080 China
- Guangzhou Hoffmann Institute of Immunology, School of Basic Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou, 510182 China
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Abstract
Gene expression frequently requires chromatin-remodeling complexes, and it is assumed that these complexes have common gene targets across cell types. Contrary to this belief, we show by genome-wide expression profiling that Bptf, an essential and unique subunit of the nucleosome-remodeling factor (NURF), predominantly regulates the expression of a unique set of genes between diverse cell types. Coincident with its functions in gene expression, we observed that Bptf is also important for regulating nucleosome occupancy at nucleosome-free regions (NFRs), many of which are located at sites occupied by the multivalent factors Ctcf and cohesin. NURF function at Ctcf binding sites could be direct, because Bptf occupies Ctcf binding sites in vivo and has physical interactions with CTCF and the cohesin subunit SA2. Assays of several Ctcf binding sites using reporter assays showed that their regulatory activity requires Bptf in two different cell types. Focused studies at H2-K1 showed that Bptf regulates the ability of Klf4 to bind near an upstream Ctcf site, possibly influencing gene expression. In combination, these studies demonstrate that gene expression as regulated by NURF occurs partly through physical and functional interactions with the ubiquitous and multivalent factors Ctcf and cohesin.
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Han BY, Wu S, Foo CS, Horton RM, Jenne CN, Watson SR, Whittle B, Goodnow CC, Cyster JG. Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment. eLife 2014; 3. [PMID: 25343476 PMCID: PMC4371841 DOI: 10.7554/elife.03549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 09/24/2014] [Indexed: 12/26/2022] Open
Abstract
The generation of naïve T lymphocytes is critical for immune function yet the
mechanisms governing their maturation remain incompletely understood. We have
identified a mouse mutant, bloto, that harbors a hypomorphic
mutation in the zinc finger protein Zfp335.
Zfp335bloto/bloto mice exhibit a naïve T cell
deficiency due to an intrinsic developmental defect that begins to manifest in the
thymus and continues into the periphery, affecting T cells that have recently
undergone thymic egress. The effects of Zfp335bloto are multigenic and
cannot be attributed to altered thymic selection, proliferation or Bcl2-dependent
survival. Zfp335 binds to promoter regions via a consensus motif, and its target
genes are enriched in categories related to protein metabolism, mitochondrial
function, and transcriptional regulation. Restoring the expression of one target,
Ankle2, partially rescues T cell maturation. These findings identify Zfp335 as a
transcription factor and essential regulator of late-stage intrathymic and
post-thymic T cell maturation. DOI:http://dx.doi.org/10.7554/eLife.03549.001 To defend our bodies against a variety of foreign microbes, our immune system makes
cells called T cells that can identify these invaders and help to destroy them. There
are several types of T cells that play different roles in the immune response: some
activate other immune cells, while others destroy cells that have been infected by
viruses or other pathogens. T cells develop in a specialized organ called the thymus, where they go through a
rigorous selection process before being released as mature T cells into the rest of
the body. This selection process includes eliminating individual T cells that are
found to be sub-standard, perhaps because they might mistake our own cells for enemy
cells. However, many of the details of the later stages of T cell development are not
fully understood. Han et al. have now found that a protein called Zfp335 that is involved in the
production of mature T cells. Mice carrying a mutation in the gene that makes this
protein have fewer mature T cells than normal mice. Han et al. also reveal that
Zfp335 is a transcription factor that can control whether or not other genes are
expressed as proteins, and further show that one of these proteins, Ankle2, has an
important role in the production of mature T cells. A next step in the work is to define exactly how Zfp335 controls the expression of
these genes. It will also be important to determine whether mutations in Zfp335
contribute to human T-cell immunodeficiency. DOI:http://dx.doi.org/10.7554/eLife.03549.002
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Affiliation(s)
- Brenda Y Han
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Shuang Wu
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Chuan-Sheng Foo
- Department of Computer Science, Stanford University, Stanford, United States
| | - Robert M Horton
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Craig N Jenne
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Susan R Watson
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Belinda Whittle
- Australian Phenomics Facility, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Chris C Goodnow
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Jason G Cyster
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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Markenscoff-Papadimitriou E, Allen WE, Colquitt BM, Goh T, Murphy KK, Monahan K, Mosley CP, Ahituv N, Lomvardas S. Enhancer interaction networks as a means for singular olfactory receptor expression. Cell 2014; 159:543-57. [PMID: 25417106 PMCID: PMC4243057 DOI: 10.1016/j.cell.2014.09.033] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 07/07/2014] [Accepted: 09/10/2014] [Indexed: 12/20/2022]
Abstract
The transcriptional activation of one out of ?2800 olfactory receptor (OR) alleles is a poorly understood process. Here, we identify a plethora of putative OR enhancers and study their in vivo activity in olfactory neurons. Distinguished by an unusual epigenetic signature, candidate OR enhancers are characterized by extensive interchromosomal interactions associated with OR transcription and share a similar pattern of transcription factor footprints. In particular, we establish the role of the transcription factor Bptf as a facilitator of both enhancer interactions and OR transcription. Our observations agree with the model whereby OR transcription occurs in the context of multiple interacting enhancers. Disruption of these interchromosomal interactions results in weak and multigenic OR expression, suggesting that the rare coincidence of numerous enhancers over a stochastically chosen OR may account for the singularity and robustness in OR transcription.
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Affiliation(s)
| | - William E Allen
- Neuroscience Graduate Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bradley M Colquitt
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tracie Goh
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Karl K Murphy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevin Monahan
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Colleen P Mosley
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stavros Lomvardas
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA.
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Xia P, Wang S, Huang G, Zhu P, Li M, Ye B, Du Y, Fan Z. WASH is required for the differentiation commitment of hematopoietic stem cells in a c-Myc-dependent manner. ACTA ACUST UNITED AC 2014; 211:2119-34. [PMID: 25225459 PMCID: PMC4172220 DOI: 10.1084/jem.20140169] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Xia et al. show that WASH deletion breaks the balance that controls self-renewal and differentiation of hematopoietic stem cells (HSCs). WASH assists the NURF complex to the promoter of c-Myc gene, and its loss perturbs LT-HSC differentiation by suppressing the transcriptional activation of c-Myc. Hematopoiesis is fully dependent on hematopoietic stem cells (HSCs) that possess the capacity to self-renew and differentiate into all blood cell lineages. WASH, Wiskott–Aldrich syndrome protein (WASP) and SCAR homologue (WASH) is involved in endosomal sorting as an actin-nucleating protein. Here, we show that conditional WASH deletion in the hematopoietic system causes defective blood production of the host, leading to severe cytopenia and rapid anemia. WASH deficiency causes the accumulation of long-term (LT)-HSCs in bone marrow and perturbs their differentiation potential to mature blood lineages. Importantly, WASH is located in the nucleus of LT-HSCs and associates with the nucleosome remodeling factor (NURF) complex. WASH assists the NURF complex to the promoter of c-Myc gene through its VCA domain-dependent nuclear actin nucleation. WASH deletion suppresses the transcriptional activation of c-Myc gene and impairs the differentiation of LT-HSCs. WASH acts as an upstream regulator to modulate c-Myc transcription for hematopoietic regulation.
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Affiliation(s)
- Pengyan Xia
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanling Huang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Li
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Buqing Ye
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Ranjan A, Mizuguchi G, FitzGerald PC, Wei D, Wang F, Huang Y, Luk E, Woodcock CL, Wu C. Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement. Cell 2013; 154:1232-45. [PMID: 24034247 DOI: 10.1016/j.cell.2013.08.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 06/04/2013] [Accepted: 08/05/2013] [Indexed: 01/31/2023]
Abstract
The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. Whereas the multisubunit chromatin remodeler SWR1 is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of SWR1 recruitment to S. cerevisiae promoters has been unclear. A sensitive assay for competitive binding of dinucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA and the adjoining nucleosome core particle, allowing discrimination of gene promoters over gene bodies. Analysis of mutants indicates that the conserved Swc2/YL1 subunit and the adenosine triphosphatase domain of Swr1 are mainly responsible for binding to substrate. SWR1 binding is enhanced on nucleosomes acetylated by the NuA4 histone acetyltransferase, but recognition of nucleosome-free and nucleosomal DNA is dominant over interaction with acetylated histones. Such hierarchical cooperation between DNA and histone signals expands the dynamic range of genetic switches, unifying classical gene regulation by DNA-binding factors with ATP-dependent nucleosome remodeling and posttranslational histone modifications.
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Affiliation(s)
- Anand Ranjan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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46
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Biddie SC, John S. Minireview: Conversing with chromatin: the language of nuclear receptors. Mol Endocrinol 2013; 28:3-15. [PMID: 24196351 DOI: 10.1210/me.2013-1247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nuclear receptors are transcription factors that are activated by physiological stimuli to bind DNA in the context of chromatin and regulate complex biological pathways. Major advances in nuclear receptor biology have been aided by genome scale examinations of receptor interactions with chromatin. In this review, we summarize the roles of the chromatin landscape in regulating nuclear receptor function. Chromatin acts as a central integrator in the nuclear receptor-signaling axis, operating in distinct temporal modalities. Chromatin effects nuclear receptor action by specifying its genomic localization and interactions with regulatory elements. On receptor binding, changes in chromatin operate as an effector of receptor signaling to modulate transcriptional events. Chromatin is therefore an integral component of the pathways that guide nuclear receptor action in cell-type-specific and cell state-dependent manners.
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Affiliation(s)
- Simon C Biddie
- Addenbrooke's Hospital (S.C.B.), Cambridge University Hospitals National Health Service Foundation Trust, Hills Road, Cambridge CB2 0QQ, United Kingdom; and National Institutes of Health (S.J.), National Cancer Institute, Laboratory for Genome Integrity, Bethesda, Maryland 20892
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47
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48
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Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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49
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Chromatin-remodeling complex specificity and embryonic vascular development. Cell Mol Life Sci 2012; 69:3921-31. [PMID: 22618247 DOI: 10.1007/s00018-012-1023-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/12/2012] [Accepted: 05/02/2012] [Indexed: 12/27/2022]
Abstract
Vascular development is a dynamic process that relies on the coordinated expression of numerous genes, but the factors that regulate gene expression during blood vessel development are not well defined. ATP-dependent chromatin-remodeling complexes are gaining attention for their specific temporal and spatial effects on gene expression during vascular development. Genetic mutations in chromatin-remodeling complex subunits are revealing roles for the complexes in vascular signaling pathways at discrete developmental time points. Phenotypic analysis of these models at various stages of vascular development will continue to expand our understanding of how chromatin remodeling impacts new blood vessel growth. Such research could also provide novel therapeutic targets for the treatment of vascular pathologies.
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50
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Wurster AL, Precht P, Becker KG, Wood WH, Zhang Y, Wang Z, Pazin MJ. IL-10 transcription is negatively regulated by BAF180, a component of the SWI/SNF chromatin remodeling enzyme. BMC Immunol 2012; 13:9. [PMID: 22336179 PMCID: PMC3313858 DOI: 10.1186/1471-2172-13-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 02/15/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND SWI/SNF chromatin remodeling enzymes play a critical role in the development of T helper lymphocytes, including Th2 cells, and directly program chromatin structure at Th2 cytokine genes. Different versions of SWI/SNF complexes, including BAF and PBAF, have been described based on unique subunit composition. However, the relative role of BAF and PBAF in Th cell function and cytokine expression has not been reported. RESULTS Here we examine the role of the PBAF SWI/SNF complex in Th cell development and gene expression using mice deficient for a PBAF-specific component, BAF180. We find that T cell development in the thymus and lymphoid periphery is largely normal when the BAF180 gene is deleted late in thymic development. However, BAF180-deficient Th2 cells express high levels of the immunoregulatory cytokine IL-10. BAF180 binds directly to regulatory elements in the Il-10 locus but is replaced by BAF250 BAF complexes in the absence of BAF180, resulting in increased histone acetylation and CBP recruitment to the IL-10 locus. CONCLUSIONS These results demonstrate that BAF180 is a repressor of IL-10 transcription in Th2 cells and suggest that the differential recruitment of different SWI/SNF subtypes can have direct consequences on chromatin structure and gene transcription.
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Affiliation(s)
- Andrea L Wurster
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, USA
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