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Oh S, Boo K, Kim J, Baek SA, Jeon Y, You J, Lee H, Choi HJ, Park D, Lee JM, Baek SH. The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes. Nucleic Acids Res 2020; 48:9037-9052. [PMID: 32735658 PMCID: PMC7498345 DOI: 10.1093/nar/gkaa626] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic regulation is important for establishing lineage-specific gene expression during early development. Although signaling pathways have been well-studied for regulation of trophectoderm reprogramming, epigenetic regulation of trophectodermal genes with histone modification dynamics have been poorly understood. Here, we identify that plant homeodomain finger protein 6 (PHF6) is a key epigenetic regulator for activation of trophectodermal genes using RNA-sequencing and ChIP assays. PHF6 acts as an E3 ubiquitin ligase for ubiquitination of H2BK120 (H2BK120ub) via its extended plant homeodomain 1 (PHD1), while the extended PHD2 of PHF6 recognizes acetylation of H2BK12 (H2BK12Ac). Intriguingly, the recognition of H2BK12Ac by PHF6 is important for exerting its E3 ubiquitin ligase activity for H2BK120ub. Together, our data provide evidence that PHF6 is crucial for epigenetic regulation of trophectodermal gene expression by linking H2BK12Ac to H2BK120ub modification.
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Affiliation(s)
- Sungryong Oh
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyungjin Boo
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jaebeom Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seon Ah Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Yoon Jeon
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Junghyun You
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, South Korea
| | - Ji Min Lee
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, South Korea
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
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Kannan-Sundhari A, Abad C, Maloof ME, Ayad NG, Young JI, Liu XZ, Walz K. Bromodomain Protein BRD4 Is Essential for Hair Cell Function and Survival. Front Cell Dev Biol 2020; 8:576654. [PMID: 33015071 PMCID: PMC7509448 DOI: 10.3389/fcell.2020.576654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022] Open
Abstract
Hair cells (HCs) play crucial roles in perceiving sound, acceleration, and fluid motion. The tonotopic architecture of the sensory epithelium recognizes mechanical stimuli and convert them into electrical signals. The expression and regulation of the genes in the inner ear is very important to keep the sensory organ functional. Our study is the first to investigate the role of the epigenetic reader Brd4 in the mouse inner ear. We demonstrate that HC specific deletion of Brd4 in vivo in the mouse inner ear is sufficient to cause profound hearing loss (HL), degeneration of stereocilia, nerve fibers and HC loss postnatally in mouse; suggesting an important role in hearing function and maintenance.
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Affiliation(s)
- Abhiraami Kannan-Sundhari
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, United States.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States
| | - Clemer Abad
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States
| | - Marie E Maloof
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Nagi G Ayad
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Juan I Young
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States.,John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States
| | - Xue Zhong Liu
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, United States.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States.,John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States
| | - Katherina Walz
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States.,John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States
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Harvey A, Caretti G, Moresi V, Renzini A, Adamo S. Interplay between Metabolites and the Epigenome in Regulating Embryonic and Adult Stem Cell Potency and Maintenance. Stem Cell Reports 2020; 13:573-589. [PMID: 31597110 PMCID: PMC6830055 DOI: 10.1016/j.stemcr.2019.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022] Open
Abstract
The environment surrounding stem cells has the ability to elicit profound, heritable epigenetic changes orchestrated by multiple epigenetic mechanisms, which can be modulated by the level of specific metabolites. In this review, we highlight the significance of metabolism in regulating stem cell homeostasis, cell state, and differentiation capacity, using metabolic regulation of embryonic and adult muscle stem cells as examples, and cast light on the interaction between cellular metabolism and epigenetics. These new regulatory networks, based on the dynamic interplay between metabolism and epigenetics in stem cell biology, are important, not only for understanding tissue homeostasis, but to determine in vitro culture conditions which accurately support normal cell physiology.
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Affiliation(s)
- Alexandra Harvey
- School of BioSciences, University of Melbourne, Parkville, VIC 2010, Australia
| | - Giuseppina Caretti
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Viviana Moresi
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome and Interuniversity Institute of Myology, Rome, Italy.
| | - Alessandra Renzini
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome and Interuniversity Institute of Myology, Rome, Italy
| | - Sergio Adamo
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome and Interuniversity Institute of Myology, Rome, Italy
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4
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Rao A, LaBonne C. Histone deacetylase activity has an essential role in establishing and maintaining the vertebrate neural crest. Development 2018; 145:dev.163386. [PMID: 30002130 DOI: 10.1242/dev.163386] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/04/2018] [Indexed: 12/24/2022]
Abstract
The neural crest, a progenitor population that drove vertebrate evolution, retains the broad developmental potential of the blastula cells it is derived from, even as neighboring cells undergo lineage restriction. The mechanisms that enable these cells to preserve their developmental potential remain poorly understood. Here, we explore the role of histone deacetylase (HDAC) activity in this process in Xenopus We show that HDAC activity is essential for the formation of neural crest, as well as for proper patterning of the early ectoderm. The requirement for HDAC activity initiates in naïve blastula cells; HDAC inhibition causes loss of pluripotency gene expression and blocks the ability of blastula stem cells to contribute to lineages of the three embryonic germ layers. We find that pluripotent naïve blastula cells and neural crest cells are both characterized by low levels of histone acetylation, and show that increasing HDAC1 levels enhance the ability of blastula cells to be reprogrammed to a neural crest state. Together, these findings elucidate a previously uncharacterized role for HDAC activity in establishing the neural crest stem cell state.
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Affiliation(s)
- Anjali Rao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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Wakeel A, Ali I, Khan AR, Wu M, Upreti S, Liu D, Liu B, Gan Y. Involvement of histone acetylation and deacetylation in regulating auxin responses and associated phenotypic changes in plants. Plant Cell Rep 2018; 37:51-59. [PMID: 28948334 DOI: 10.1007/s00299-017-2205-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/05/2017] [Indexed: 05/04/2023]
Abstract
The most recent outcomes about the transcription factors and transcription complexes mediated auxin signaling pathway by the histone acetylation and deacetylation. The phytohormone auxin, is required to regulate its accumulation spatiotemporally and responses to orchestrate various developmental levels in plants. Histone acetylation and deacetylation modulate auxin biosynthesis, its distribution and accumulation. In the absence of auxin, histone deacetylase represses the expression of auxin-responsive genes. Various transcription factors and transcription complexes facilitate the proper regulation of auxin signaling pathway genes. The primary and lateral root development, promotion of flowering and initiation of seed germination are all regulated by auxin-mediated histone acetylation and deacetylation. These findings conclude the auxin mode of action, which is mediated by histone acetylation and deacetylation, and associated phenotypic responses in plants, along with the underlying mechanism of these modifications.
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Affiliation(s)
- Abdul Wakeel
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Ali
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ali Raza Khan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Minjie Wu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sakila Upreti
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Dongdong Liu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bohan Liu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
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7
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Abstract
Regenerative medicine, ranging from stem cell therapy to organ regeneration, is promising to revolutionize treatments of diseases and aging. These approaches require a perfect understanding of cell reprogramming and differentiation. Predictive modeling of cellular systems has the potential to provide insights about the dynamics of cellular processes, and guide their control. Moreover in many cases, it provides alternative to experimental tests, difficult to perform for practical or ethical reasons. The variety and accuracy of biological processes represented in mathematical models grew in-line with the discovery of underlying molecular mechanisms. High-throughput data generation led to the development of models based on data analysis, as an alternative to more established modeling based on prior mechanistic knowledge. In this chapter, we give an overview of existing mathematical models of pluripotency and cell fate, to illustrate the variety of methods and questions. We conclude that current approaches are yet to overcome a number of limitations: Most of the computational models have so far focused solely on understanding the regulation of pluripotency, and the differentiation of selected cell lineages. In addition, models generally interrogate only a few biological processes. However, a better understanding of the reprogramming process leading to ESCs and iPSCs is required to improve stem-cell therapies. One also needs to understand the links between signaling, metabolism, regulation of gene expression, and the epigenetics machinery.
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Affiliation(s)
- Pınar Pir
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Nicolas Le Novère
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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Li C, Guo S, Zhang M, Gao J, Guo Y. DNA methylation and histone modification patterns during the late embryonic and early postnatal development of chickens. Poult Sci 2015; 94:706-21. [PMID: 25691759 DOI: 10.3382/ps/pev016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Early mammalian embryonic cells have been proven to be essential for embryonic development and the health of neonates. A series of epigenetic reprogramming events, including DNA methylation and histone modifications, occur during early embryonic development. However, epigenetic marks in late embryos and neonates are not well understood, especially in avian species. To investigate the epigenetic patterns of developing embryos and posthatched chicks, embryos at embryonic day 5 (E5), E8, E11, E14, E17, and E20 and newly hatched chicks on day of life 1 (D1), D7, D14, D21 were collected. The levels of global DNA methylation and histone H3 at lysine 9 residue (H3K9) modifications were measured in samples of liver, jejunum, and breast skeletal muscles by Western blotting and immunofluorescence staining. According to our data, decreased levels of proliferating cell nuclear antigen expression were found in the liver and a V-shaped pattern of proliferating cell nuclear antigen expression was found in the jejunum. The level of proliferating cell nuclear antigen in muscle was relatively stable. Caspase 3 expression gradually decreased over time in liver, was stable in the jejunum, and increased in muscle. Levels of DNA methylation and H3K9 acetylation decreased in liver over time, while the pattern was N-shaped in jejunal tissue and W-shaped in pectoral muscles, and these changes were accompanied by dynamic changes of DNA methyltransferases, histone acetyltransferases 1, and histone deacetylase 2. Moreover, dimethylation, trimethylation, and acetylation of H3K9 were expressed in a time- and tissue-dependent manner. After birth, epigenetic marks were relatively stable and found at lower levels. These results indicate that spatiotemporal specific epigenetic alterations could be critical for the late development of chick embryos and neonates.
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Affiliation(s)
- Changwu Li
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
| | - Shuangshuang Guo
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
| | - Ming Zhang
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
| | - Jing Gao
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
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9
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Suehiro JI, Kanki Y, Makihara C, Schadler K, Miura M, Manabe Y, Aburatani H, Kodama T, Minami T. Genome-wide approaches reveal functional vascular endothelial growth factor (VEGF)-inducible nuclear factor of activated T cells (NFAT) c1 binding to angiogenesis-related genes in the endothelium. J Biol Chem 2014; 289:29044-59. [PMID: 25157100 DOI: 10.1074/jbc.m114.555235] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
VEGF is a key regulator of endothelial cell migration, proliferation, and inflammation, which leads to activation of several signaling cascades, including the calcineurin-nuclear factor of activated T cells (NFAT) pathway. NFAT is not only important for immune responses but also for cardiovascular development and the pathogenesis of Down syndrome. By using Down syndrome model mice and clinical patient samples, we showed recently that the VEGF-calcineurin-NFAT signaling axis regulates tumor angiogenesis and tumor metastasis. However, the connection between genome-wide views of NFAT-mediated gene regulation and downstream gene function in the endothelium has not been studied extensively. Here we performed comprehensive mapping of genome-wide NFATc1 binding in VEGF-stimulated primary cultured endothelial cells and elucidated the functional consequences of VEGF-NFATc1-mediated phenotypic changes. A comparison of the NFATc1 ChIP sequence profile and epigenetic histone marks revealed that predominant NFATc1-occupied peaks overlapped with promoter-associated histone marks. Moreover, we identified two novel NFATc1 regulated genes, CXCR7 and RND1. CXCR7 knockdown abrogated SDF-1- and VEGF-mediated cell migration and tube formation. siRNA treatment of RND1 impaired vascular barrier function, caused RhoA hyperactivation, and further stimulated VEGF-mediated vascular outgrowth from aortic rings. Taken together, these findings suggest that dynamic NFATc1 binding to target genes is critical for VEGF-mediated endothelial cell activation. CXCR7 and RND1 are NFATc1 target genes with multiple functions, including regulation of cell migration, tube formation, and barrier formation in endothelial cells.
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Affiliation(s)
| | - Yasuharu Kanki
- From the Division of Vascular Biology, Systems Biology, The Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904 Japan and
| | | | - Keri Schadler
- From the Division of Vascular Biology, the Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Mai Miura
- From the Division of Vascular Biology
| | | | | | - Tatsuhiko Kodama
- Systems Biology, The Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904 Japan and
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10
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Vieira PA, Lovelace JW, Corches A, Rashid AJ, Josselyn SA, Korzus E. Prefrontal consolidation supports the attainment of fear memory accuracy. ACTA ACUST UNITED AC 2014; 21:394-405. [PMID: 25031365 PMCID: PMC4105719 DOI: 10.1101/lm.036087.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The neural mechanisms underlying the attainment of fear memory accuracy for appropriate discriminative responses to aversive and nonaversive stimuli are unclear. Considerable evidence indicates that coactivator of transcription and histone acetyltransferase cAMP response element binding protein (CREB) binding protein (CBP) is critically required for normal neural function. CBP hypofunction leads to severe psychopathological symptoms in human and cognitive abnormalities in genetic mutant mice with severity dependent on the neural locus and developmental time of the gene inactivation. Here, we showed that an acute hypofunction of CBP in the medial prefrontal cortex (mPFC) results in a disruption of fear memory accuracy in mice. In addition, interruption of CREB function in the mPFC also leads to a deficit in auditory discrimination of fearful stimuli. While mice with deficient CBP/CREB signaling in the mPFC maintain normal responses to aversive stimuli, they exhibit abnormal responses to similar but nonrelevant stimuli when compared to control animals. These data indicate that improvement of fear memory accuracy involves mPFC-dependent suppression of fear responses to nonrelevant stimuli. Evidence from a context discriminatory task and a newly developed task that depends on the ability to distinguish discrete auditory cues indicated that CBP-dependent neural signaling within the mPFC circuitry is an important component of the mechanism for disambiguating the meaning of fear signals with two opposing values: aversive and nonaversive.
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Affiliation(s)
- Philip A Vieira
- Department of Psychology and Neuroscience Program, University of California Riverside, California 92521, USA
| | - Jonathan W Lovelace
- Department of Psychology and Neuroscience Program, University of California Riverside, California 92521, USA
| | - Alex Corches
- Biomedical Sciences Program, University of California Riverside, California 92521, USA
| | - Asim J Rashid
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Sheena A Josselyn
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Edward Korzus
- Department of Psychology and Neuroscience Program, University of California Riverside, California 92521, USA Biomedical Sciences Program, University of California Riverside, California 92521, USA
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Legartová S, Kozubek S, Franek M, Zdráhal Z, Lochmanová G, Martinet N, Bártová E. Cell differentiation along multiple pathways accompanied by changes in histone acetylation status. Biochem Cell Biol 2014; 92:85-93. [DOI: 10.1139/bcb-2013-0082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Post-translational modification of histones is fundamental to the regulation of basic nuclear processes and subsequent cellular events, including differentiation. In this study, we analyzed acetylated forms of histones H2A, H2B, and H4 during induced differentiation in mouse (mESCs) and human (hESCs) embryonic stem cells and during induced enterocytic differentiation of colon cancer cells in vitro. Endoderm-like differentiation of mESCs induced by retinoic acid and enterocytic differentiation induced by histone deacetylase inhibitor sodium butyrate were accompanied by increased mono-, di-, and tri-acetylation of histone H2B and a pronounced increase in di- and tri-acetylation of histone H4. In enterocytes, mono-acetylation of histone H2A also increased and tetra-acetylation of histone H4 appeared only after induction of this differentiation pathway. During differentiation of hESCs, we observed increased mono-acetylation and decreased tri-acetylation of H2B. Mono-, di-, and tri-acetylation of H4 were reduced, manifested by a significant increase in nonacetylated H4 histones. Levels of acetylated histones increased during induced differentiation in mESCs and during histone deacetylase (HDAC) inhibitor-induced enterocytic differentiation, whereas differentiation of human ESCs was associated with reduced acetylation of histones H2B and H4.
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Affiliation(s)
- Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Franek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Research Group – Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 753/5 Brno, Czech Republic
| | - Gabriela Lochmanová
- Research Group – Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 753/5 Brno, Czech Republic
| | - Nadine Martinet
- Institut de Chimie, Université de Nice Sophia Antipolis-UMR CNRS 7272, Parc Valrose, 06100 Nice, France
| | - Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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Abstract
We consider the problem of quantifying temporal coordination between multiple high-dimensional responses. We introduce a family of multi-way stochastic blockmodels suited for this problem, which avoids pre-processing steps such as binning and thresholding commonly adopted for this type of problems, in biology. We develop two inference procedures based on collapsed Gibbs sampling and variational methods. We provide a thorough evaluation of the proposed methods on simulated data, in terms of membership and blockmodel estimation, predictions out-of-sample, and run-time. We also quantify the effects of censoring procedures such as binning and thresholding on the estimation tasks. We use these models to carry out an empirical analysis of the functional mechanisms driving the coordination between gene expression and metabolite concentrations during carbon and nitrogen starvation, in S. cerevisiae.
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13
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Tanida T, Tasaka K, Akahoshi E, Ishihara-Sugano M, Saito M, Kawata S, Danjo M, Tokumoto J, Mantani Y, Nagahara D, Tabuchi Y, Yokoyama T, Kitagawa H, Kawata M, Hoshi N. Fetal exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin transactivates aryl hydrocarbon receptor-responsive element III in the tyrosine hydroxylase immunoreactive neurons of the mouse midbrain. J Appl Toxicol 2013; 34:117-26. [DOI: 10.1002/jat.2839] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/16/2012] [Accepted: 10/16/2012] [Indexed: 01/03/2023]
Affiliation(s)
- Takashi Tanida
- Department of Anatomy and Neurobiology; Kyoto Prefectural University of Medicine; Kawaramachi Hirokoji, Kamigyo-ku Kyoto 602-8566 Japan
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
| | - Ken Tasaka
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
| | - Eiichi Akahoshi
- Frontier Research Laboratory, Corporate Research and Development Center; Toshiba Corporation; 1 Komukai-Toshiba cho, Saiwai Kawasaki 212-8582 Japan
| | - Mitsuko Ishihara-Sugano
- Frontier Research Laboratory, Corporate Research and Development Center; Toshiba Corporation; 1 Komukai-Toshiba cho, Saiwai Kawasaki 212-8582 Japan
| | - Michiko Saito
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences; Nara Institute of Science and Technology; 8916-5 Takayama, Ikoma Nara 630-0192 Japan
| | - Shigehisa Kawata
- Laboratory of Molecular Oncology, Graduate School of Biological Sciences; Nara Institute of Science and Technology; 8916-5 Takayama, Ikoma Nara 630-0192 Japan
| | - Megumi Danjo
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
| | - Junko Tokumoto
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
| | - Youhei Mantani
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
| | - Daichi Nagahara
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
| | - Yoshiaki Tabuchi
- Division of Molecular Genetics Research, Life Science Research Center; University of Toyama; 2630 Sugitani Toyama 930-0194 Japan
| | - Toshifumi Yokoyama
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
| | - Hiroshi Kitagawa
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
| | - Mitsuhiro Kawata
- Department of Anatomy and Neurobiology; Kyoto Prefectural University of Medicine; Kawaramachi Hirokoji, Kamigyo-ku Kyoto 602-8566 Japan
| | - Nobuhiko Hoshi
- Department of Animal Science, Graduate School of Agricultural Science; Kobe University; 1-1 Rokkodai cho, Nada Kobe 657-8501 Japan
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Manzano C, Ramirez-Parra E, Casimiro I, Otero S, Desvoyes B, De Rybel B, Beeckman T, Casero P, Gutierrez C, C. del Pozo J. Auxin and epigenetic regulation of SKP2B, an F-box that represses lateral root formation. Plant Physiol 2012; 160:749-62. [PMID: 22837358 PMCID: PMC3461553 DOI: 10.1104/pp.112.198341] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In plants, lateral roots originate from pericycle founder cells that are specified at regular intervals along the main root. Here, we show that Arabidopsis (Arabidopsis thaliana) SKP2B (for S-Phase Kinase-Associated Protein2B), an F-box protein, negatively regulates cell cycle and lateral root formation as it represses meristematic and founder cell divisions. According to its function, SKP2B is expressed in founder cells, lateral root primordia and the root apical meristem. We identified a novel motif in the SKP2B promoter that is required for its specific root expression and auxin-dependent induction in the pericycle cells. Next to a transcriptional control by auxin, SKP2B expression is regulated by histone H3.1/H3.3 deposition in a CAF-dependent manner. The SKP2B promoter and the 5' end of the transcribed region are enriched in H3.3, which is associated with active chromatin states, over H3.1. Furthermore, the SKP2B promoter is also regulated by H3 acetylation in an auxin- and IAA14-dependent manner, reinforcing the idea that epigenetics represents an important regulatory mechanism during lateral root formation.
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Geeven G, van Kesteren RE, Smit AB, de Gunst MCM. Identification of context-specific gene regulatory networks with GEMULA--gene expression modeling using LAsso. ACTA ACUST UNITED AC 2011; 28:214-21. [PMID: 22106333 DOI: 10.1093/bioinformatics/btr641] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
MOTIVATION Gene regulatory networks, in which edges between nodes describe interactions between transcriptional regulators and their target genes, determine the coordinated spatiotemporal expression of genes. Especially in higher organisms, context-specific combinatorial regulation by transcription factors (TFs) is believed to determine cellular states and fates. TF-target gene interactions can be studied using high-throughput techniques such as ChIP-chip or ChIP-Seq. These experiments are time and cost intensive, and further limited by, for instance, availability of high affinity TF antibodies. Hence, there is a practical need for methods that can predict TF-TF and TF-target gene interactions in silico, i.e. from gene expression and DNA sequence data alone. We propose GEMULA, a novel approach based on linear models to predict TF-gene expression associations and TF-TF interactions from experimental data. GEMULA is based on linear models, fast and considers a wide range of biologically plausible models that describe gene expression data as a function of predicted TF binding to gene promoters. RESULTS We show that models inferred with GEMULA are able to explain roughly 70% of the observed variation in gene expression in the yeast heat shock response. The functional relevance of the inferred TF-TF interactions in these models are validated by different sources of independent experimental evidence. We also have applied GEMULA to an in vitro model of neuronal outgrowth. Our findings confirm existing knowledge on gene regulatory interactions underlying neuronal outgrowth, but importantly also generate new insights into the temporal dynamics of this gene regulatory network that can now be addressed experimentally. AVAILABILITY The GEMULA R-package is available from http://www.few.vu.nl/~degunst/gemula_1.0.tar.gz.
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Affiliation(s)
- Geert Geeven
- Department of Mathematics, Faculty of Sciences, Neuroscience Campus Amsterdam, VU University, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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Martinez-Outschoorn UE, Prisco M, Ertel A, Tsirigos A, Lin Z, Pavlides S, Wang C, Flomenberg N, Knudsen ES, Howell A, Pestell RG, Sotgia F, Lisanti MP. Ketones and lactate increase cancer cell "stemness," driving recurrence, metastasis and poor clinical outcome in breast cancer: achieving personalized medicine via Metabolo-Genomics. Cell Cycle 2011; 10:1271-86. [PMID: 21512313 DOI: 10.4161/cc.10.8.15330] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Previously, we showed that high-energy metabolites (lactate and ketones) "fuel" tumor growth and experimental metastasis in an in vivo xenograft model, most likely by driving oxidative mitochondrial metabolism in breast cancer cells. To mechanistically understand how these metabolites affect tumor cell behavior, here we used genome-wide transcriptional profiling. Briefly, human breast cancer cells (MCF7) were cultured with lactate or ketones, and then subjected to transcriptional analysis (exon-array). Interestingly, our results show that treatment with these high-energy metabolites increases the transcriptional expression of gene profiles normally associated with "stemness," including genes upregulated in embryonic stem (ES) cells. Similarly, we observe that lactate and ketones promote the growth of bonafide ES cells, providing functional validation. The lactate- and ketone-induced "gene signatures" were able to predict poor clinical outcome (including recurrence and metastasis) in a cohort of human breast cancer patients. Taken together, our results are consistent with the idea that lactate and ketone utilization in cancer cells promotes the "cancer stem cell" phenotype, resulting in significant decreases in patient survival. One possible mechanism by which these high-energy metabolites might induce stemness is by increasing the pool of Acetyl-CoA, leading to increased histone acetylation, and elevated gene expression. Thus, our results mechanistically imply that clinical outcome in breast cancer could simply be determined by epigenetics and energy metabolism, rather than by the accumulation of specific "classical" gene mutations. We also suggest that high-risk cancer patients (identified by the lactate/ketone gene signatures) could be treated with new therapeutics that target oxidative mitochondrial metabolism, such as the anti-oxidant and "mitochondrial poison" metformin. Finally, we propose that this new approach to personalized cancer medicine be termed "Metabolo-Genomics," which incorporates features of both 1) cell metabolism and 2) gene transcriptional profiling. Importantly, this powerful new approach directly links cancer cell metabolism with clinical outcome, and new therapeutic strategies for inhibiting the TCA cycle and mitochondrial oxidative phosphorylation in cancer cells.
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Affiliation(s)
- Ubaldo E Martinez-Outschoorn
- The Jefferson Stem Cell Biology and Regenerative Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
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