51
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Budnick I, Hamburg-Shields E, Chen D, Torre E, Jarrell A, Akhtar-Zaidi B, Cordovan O, Spitale RC, Scacheri P, Atit RP. Defining the identity of mouse embryonic dermal fibroblasts. Genesis 2016; 54:415-30. [PMID: 27265328 DOI: 10.1002/dvg.22952] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 01/14/2023]
Abstract
Embryonic dermal fibroblasts in the skin have the exceptional ability to initiate hair follicle morphogenesis and contribute to scarless wound healing. Activation of the Wnt signaling pathway is critical for dermal fibroblast fate selection and hair follicle induction. In humans, mutations in Wnt pathway components and target genes lead to congenital focal dermal hypoplasias with diminished hair. The gene expression signature of embryonic dermal fibroblasts during differentiation and its dependence on Wnt signaling is unknown. Here we applied Shannon entropy analysis to identify the gene expression signature of mouse embryonic dermal fibroblasts. We used available human DNase-seq and histone modification ChiP-seq data on various cell-types to demonstrate that genes in the fibroblast cell identity signature can be epigenetically repressed in other cell-types. We found a subset of the signature genes whose expression is dependent on Wnt/β-catenin activity in vivo. With our approach, we have defined and validated a statistically derived gene expression signature that may mediate dermal fibroblast identity and function in development and disease. genesis 54:415-430, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Isadore Budnick
- Department of Biology, Case Western Reserve University, Cleveland, Ohio
| | | | - Demeng Chen
- Department of Biology, Case Western Reserve University, Cleveland, Ohio
| | - Eduardo Torre
- Epithelial Biology Program, Department of Dermatology, Stanford University, California
| | - Andrew Jarrell
- Department of Biology, Case Western Reserve University, Cleveland, Ohio
| | - Batool Akhtar-Zaidi
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | - Olivia Cordovan
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | - Rob C Spitale
- Epithelial Biology Program, Department of Dermatology, Stanford University, California.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Peter Scacheri
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | - Radhika P Atit
- Department of Biology, Case Western Reserve University, Cleveland, Ohio.,Department of Pharmaceutical Sciences, University of California, Irvine, California.,Department of Dermatology, Case Western Reserve University, Cleveland, Ohio
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52
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Schierding W, Antony J, Cutfield WS, Horsfield JA, O'Sullivan JM. Intergenic GWAS SNPs are key components of the spatial and regulatory network for human growth. Hum Mol Genet 2016; 25:3372-3382. [PMID: 27288450 DOI: 10.1093/hmg/ddw165] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/19/2016] [Accepted: 05/20/2016] [Indexed: 12/25/2022] Open
Abstract
Meta-analysis of genome-wide association studies has resulted in the identification of hundreds of genetic variants associated with growth and stature. Determining how these genetic variants influence growth is important, but most are non-coding, and there is little understanding of how these variants contribute to adult height. To determine the mechanisms by which human variation contributes to growth, we combined spatial genomic connectivity (high-throughput conformation capture) with functional (gene expression, expression Quantitative Trait Loci) data to determine how non-genic loci associated with infant length, pubertal and adult height and contribute to gene regulatory networks. This approach identified intergenic single-nucleotide polymorphisms (SNPs) ∼85 kb upstream of FBXW11 that spatially connect with distant loci. These regulatory connections are reinforced by evidence of SNP-enhancer effects and altered expression in genes influencing the action of human growth hormone. Functional assays provided evidence for enhancer activity of the intergenic region near FBXW11 that harbors SNP rs12153391, which is associated with an expression Quantitative Trait Loci. Our results suggest that variants in this locus have genome-wide effects as key modifiers of growth (both overgrowth and short stature) acting through a regulatory network. We believe that the genes and pathways connected with this regulatory network are potential targets that could be investigated for diagnostic, prenatal and carrier testing for growth disorders. Finally, the regulatory networks we generated illustrate the power of using existing datasets to interrogate the contribution of intergenic SNPs to common syndromes/diseases.
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Affiliation(s)
- William Schierding
- Liggins Institute, University of Auckland, Grafton, Auckland 1032, New Zealand
| | - Jisha Antony
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin 9016, New Zealand
| | - Wayne S Cutfield
- Liggins Institute, University of Auckland, Grafton, Auckland 1032, New Zealand.,Gravida: National Centre for Growth and Development, University of Auckland, Auckland 1032, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin 9016, New Zealand.,Gravida: National Centre for Growth and Development, University of Auckland, Auckland 1032, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Grafton, Auckland 1032, New Zealand, .,Gravida: National Centre for Growth and Development, University of Auckland, Auckland 1032, New Zealand
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53
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Pieraccioli M, Nicolai S, Antonov A, Somers J, Malewicz M, Melino G, Raschellà G. ZNF281 contributes to the DNA damage response by controlling the expression of XRCC2 and XRCC4. Oncogene 2016; 35:2592-601. [PMID: 26300006 DOI: 10.1038/onc.2015.320] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/02/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022]
Abstract
ZNF281 is a zinc-finger factor involved in the control of cellular stemness and epithelial-mesenchymal transition (EMT). Here, we report that ZNF281 expression increased after genotoxic stress caused by DNA-damaging drugs. Comet assays demonstrated that DNA repair was delayed in cells silenced for the expression of ZNF281 and treated with etoposide. Furthermore, the expression of 10 DNA damage response genes was downregulated in cells treated with etoposide and silenced for ZNF281. In line with this finding, XRCC2 and XRCC4, two genes that take part in homologous recombination and non-homologous end joining, respectively, were transcriptionally activated by ZNF281 through a DNA-binding-dependent mechanism, as demonstrated by luciferase assays and Chromatin crosslinking ImmunoPrecipitation experiments. c-Myc, which also binds to the promoters of XRCC2 and XRCC4, was unable to promote their transcription or to modify ZNF281 activity. Of interest, bioinformatic analysis of 1971 breast cancer patients disclosed a significant correlation between the expression of ZNF281 and that of XRCC2. In summary, our data highlight, for the first time, the involvement of ZNF281 in the cellular response to genotoxic stress through the control exercised on the expression of genes that act in different repair mechanisms.
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Affiliation(s)
- M Pieraccioli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - S Nicolai
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - A Antonov
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
| | - J Somers
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
| | - M Malewicz
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
| | - G Melino
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
| | - G Raschellà
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
- Radiation Biology and Human Health Unit, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) Research Center Casaccia, Rome, Italy
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54
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Lee BK, Shen W, Lee J, Rhee C, Chung H, Kim KY, Park IH, Kim J. Tgif1 Counterbalances the Activity of Core Pluripotency Factors in Mouse Embryonic Stem Cells. Cell Rep 2015; 13:52-60. [PMID: 26411691 DOI: 10.1016/j.celrep.2015.08.067] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/24/2015] [Accepted: 08/24/2015] [Indexed: 11/16/2022] Open
Abstract
Core pluripotency factors, such as Oct4, Sox2, and Nanog, play important roles in maintaining embryonic stem cell (ESC) identity by autoregulatory feedforward loops. Nevertheless, the mechanism that provides precise control of the levels of the ESC core factors without indefinite amplification has remained elusive. Here, we report the direct repression of core pluripotency factors by Tgif1, a previously known terminal repressor of TGFβ/activin/nodal signaling. Overexpression of Tgif1 reduces the levels of ESC core factors, whereas its depletion leads to the induction of the pluripotency factors. We confirm the existence of physical associations between Tgif1 and Oct4, Nanog, and HDAC1/2 and further show the level of Tgif1 is not significantly altered by treatment with an activator/inhibitor of the TGFβ/activin/nodal signaling. Collectively, our findings establish Tgif1 as an integral member of the core regulatory circuitry of mouse ESCs that counterbalances the levels of the core pluripotency factors in a TGFβ/activin/nodal-independent manner.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Wenwen Shen
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA
| | - Jiwoon Lee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Catherine Rhee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Haewon Chung
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA.
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55
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Kalkan T, Smith A. Mapping the route from naive pluripotency to lineage specification. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0540. [PMID: 25349449 PMCID: PMC4216463 DOI: 10.1098/rstb.2013.0540] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In the mouse blastocyst, epiblast cells are newly formed shortly before implantation. They possess a unique developmental plasticity, termed naive pluripotency. For development to proceed, this naive state must be subsumed by multi-lineage differentiation within 72 h following implantation. In vitro differentiation of naive embryonic stem cells (ESCs) cultured in controlled conditions provides a tractable system to dissect and understand the process of exit from naive pluripotency and entry into lineage specification. Exploitation of this system in recent large-scale RNAi and mutagenesis screens has uncovered multiple new factors and modules that drive or facilitate progression out of the naive state. Notably, these studies show that the transcription factor network that governs the naive state is rapidly dismantled prior to upregulation of lineage specification markers, creating an intermediate state that we term formative pluripotency. Here, we summarize these findings and propose a road map for state transitions in ESC differentiation that reflects the orderly dynamics of epiblast progression in the embryo.
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Affiliation(s)
- Tüzer Kalkan
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Austin Smith
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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56
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Abstract
Growing knowledge concerning transcriptional control of cellular pluripotency has led to the discovery that the fate of differentiated cells can be reversed, which has resulted in the generation, by means of genetic manipulation, of induced pluripotent stem cells. Overexpression of just four pluripotency-related transcription factors, namely Oct3/4, Sox2, Klf4, and c-Myc (Yamanaka factors, OKSM), in fibroblasts appears sufficient to produce this new cell type. Currently, we know that these factors induce several changes in genetic program of differentiated cells that can be divided in two general phases: the initial one is stochastic, and the subsequent one is highly hierarchical and organised. This review briefly discusses the molecular events leading to induction of pluripotency in response to forced presence of OKSM factors in somatic cells. We also discuss other reprogramming strategies used thus far as well as the advantages and disadvantages of laboratory approaches towards pluripotency induction in different cell types.
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57
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Abstract
Pluripotent cells in embryos are situated near the apex of the hierarchy of developmental potential. They are capable of generating all cell types of the mammalian body proper. Therefore, they are the exemplar of stem cells. In vivo, pluripotent cells exist transiently and become expended within a few days of their establishment. Yet, when explanted into artificial culture conditions, they can be indefinitely propagated in vitro as pluripotent stem cell lines. A host of transcription factors and regulatory genes are now known to underpin the pluripotent state. Nonetheless, how pluripotent cells are equipped with their vast multilineage differentiation potential remains elusive. Consensus holds that pluripotency transcription factors prevent differentiation by inhibiting the expression of differentiation genes. However, this does not explain the developmental potential of pluripotent cells. We have presented another emergent perspective, namely, that pluripotency factors function as lineage specifiers that enable pluripotent cells to differentiate into specific lineages, therefore endowing pluripotent cells with their multilineage potential. Here we provide a comprehensive overview of the developmental biology, transcription factors, and extrinsic signaling associated with pluripotent cells, and their accompanying subtypes, in vitro heterogeneity and chromatin states. Although much has been learned since the appreciation of mammalian pluripotency in the 1950s and the derivation of embryonic stem cell lines in 1981, we will specifically emphasize what currently remains unclear. However, the view that pluripotency factors capacitate differentiation, recently corroborated by experimental evidence, might perhaps address the long-standing question of how pluripotent cells are endowed with their multilineage differentiation potential.
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Affiliation(s)
- Kyle M. Loh
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
| | - Bing Lim
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
| | - Lay Teng Ang
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
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58
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Zhang J, Liu G, Ruan Y, Wang J, Zhao K, Wan Y, Liu B, Zheng H, Peng T, Wu W, He P, Hu FQ, Jian R. Dax1 and Nanog act in parallel to stabilize mouse embryonic stem cells and induced pluripotency. Nat Commun 2014; 5:5042. [PMID: 25284313 PMCID: PMC4205889 DOI: 10.1038/ncomms6042] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 08/20/2014] [Indexed: 12/20/2022] Open
Abstract
Nanog expression is heterogeneous and dynamic in embryonic stem cells (ESCs). However, the mechanism for stabilizing pluripotency during the transitions between Nanog(high) and Nanog(low) states is not well understood. Here we report that Dax1 acts in parallel with Nanog to regulate mouse ESC (mESCs) identity. Dax1 stable knockdown mESCs are predisposed towards differentiation but do not lose pluripotency, whereas Dax1 overexpression supports LIF-independent self-renewal. Although partially complementary, Dax1 and Nanog function independently and cannot replace one another. They are both required for full reprogramming to induce pluripotency. Importantly, Dax1 is indispensable for self-renewal of Nanog(low) mESCs. Moreover, we report that Dax1 prevents extra-embryonic endoderm (ExEn) commitment by directly repressing Gata6 transcription. Dax1 may also mediate inhibition of trophectoderm differentiation independent or as a downstream effector of Oct4. These findings establish a basal role of Dax1 in maintaining pluripotency during the state transition of mESCs and somatic cell reprogramming.
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Affiliation(s)
- Junlei Zhang
- Department of Microbiology, Third Military Medical University, Chongqing 400038, China
| | - Gaoke Liu
- Department of Microbiology, Third Military Medical University, Chongqing 400038, China
| | - Yan Ruan
- Department of Pathogenic Biology, Third Military Medical University, Chongqing 400038, China
| | - Jiali Wang
- Department of Physiology, Third Military Medical University, Chongqing 400038, China
| | - Ke Zhao
- Laboratory of Oncology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 400038, China
| | - Ying Wan
- 1] Biomedical Analysis Center, Third Military Medical University, Chongqing 100071, China [2] Department of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Bing Liu
- Laboratory of Oncology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 400038, China
| | - Hongting Zheng
- Department of Endocrinology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Tao Peng
- Research Center of Laboratory Medicine, Chengdu Military General Hospital, Sichuan 610083, China
| | - Wei Wu
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Ping He
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Fu-Quan Hu
- Department of Microbiology, Third Military Medical University, Chongqing 400038, China
| | - Rui Jian
- Department of Pathogenic Biology, Third Military Medical University, Chongqing 400038, China
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59
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Hahn S, Hermeking H. ZNF281/ZBP-99: a new player in epithelial-mesenchymal transition, stemness, and cancer. J Mol Med (Berl) 2014; 92:571-81. [PMID: 24838609 DOI: 10.1007/s00109-014-1160-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/04/2014] [Accepted: 04/25/2014] [Indexed: 12/16/2022]
Abstract
Epithelial-mesenchymal transition (EMT) represents an important mechanism during development and wound healing, and its deregulation has been implicated in metastasis. Recently, the Krüppel-type zinc-finger transcription factor ZNF281 has been characterized as an EMT-inducing transcription factor (EMT-TF). Expression of ZNF281 is induced by the EMT-TF SNAIL and inhibited by the tumor suppressive microRNA miR-34a, which mediates repression of ZNF281 by the p53 tumor suppressor. Therefore, SNAIL, miR-34a and ZNF281 form a feed-forward regulatory loop, which controls EMT. Deregulation of this circuitry by mutational and epigenetic alterations in the p53/miR-34a axis promotes colorectal cancer (CRC) progression and metastasis formation. As ZNF281 physically interacts with the transcription factors NANOG, OCT4, SOX2, and c-MYC, it has been implicated in the regulation of pluripotency, stemness, and cancer. Accordingly, ectopic ZNF281 expression in CRC lines induces the stemness markers LGR5 and CD133 and promotes sphere formation, suggesting that the elevated expression of ZNF281 detected in cancer may enhance tumor stem cell formation and/or function. Here, we review the functional and organismal studies of ZNF281/ZBP-99 and its close relative ZBP-89/ZFP148 reported so far. Taken together, ZNF281 related biology has the potential to be translated into cancer diagnostic, prognostic, and therapeutic approaches.
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Affiliation(s)
- Stefanie Hahn
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Strasse 36, 80337, Munich, Germany
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60
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Saunders A, Faiola F, Wang J. Concise review: pursuing self-renewal and pluripotency with the stem cell factor Nanog. Stem Cells 2014; 31:1227-36. [PMID: 23653415 DOI: 10.1002/stem.1384] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/04/2013] [Indexed: 01/06/2023]
Abstract
Pluripotent embryonic stem cells and induced pluripotent stem cells hold great promise for future use in tissue replacement therapies due to their ability to self-renew indefinitely and to differentiate into all adult cell types. Harnessing this therapeutic potential efficiently requires a much deeper understanding of the molecular processes at work within the pluripotency network. The transcription factors Nanog, Oct4, and Sox2 reside at the core of this network, where they interact and regulate their own expression as well as that of numerous other pluripotency factors. Of these core factors, Nanog is critical for blocking the differentiation of pluripotent cells, and more importantly, for establishing the pluripotent ground state during somatic cell reprogramming. Both mouse and human Nanog are able to form dimers in vivo, allowing them to preferentially interact with certain factors and perform unique functions. Recent studies have identified an evolutionary functional conservation among vertebrate Nanog orthologs from chick, zebrafish, and the axolotl salamander, adding an additional layer of complexity to Nanog function. Here, we present a detailed overview of published work focusing on Nanog structure, function, dimerization, and regulation at the genetic and post-translational levels with regard to the establishment and maintenance of pluripotency. The full spectrum of Nanog function in pluripotent stem cells and in cancer is only beginning to be revealed. We therefore use this evidence to advocate for more comprehensive analysis of Nanog in the context of disease, development, and regeneration.
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Affiliation(s)
- Arven Saunders
- Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, New York, NY, USA
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61
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Levinson M, Zhou Q. A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes. ACTA ACUST UNITED AC 2014; 30:636-43. [PMID: 24115169 DOI: 10.1093/bioinformatics/btt585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Cellular processes are controlled, directly or indirectly, by the binding of hundreds of different DNA binding factors (DBFs) to the genome. One key to deeper understanding of the cell is discovering where, when and how strongly these DBFs bind to the DNA sequence. Direct measurement of DBF binding sites (BSs; e.g. through ChIP-Chip or ChIP-Seq experiments) is expensive, noisy and not available for every DBF in every cell type. Naive and most existing computational approaches to detecting which DBFs bind in a set of genomic regions of interest often perform poorly, due to the high false discovery rates and restrictive requirements for prior knowledge. RESULTS We develop SparScape, a penalized Bayesian method for identifying DBFs active in the considered regions and predicting a joint probabilistic binding landscape. Using a sparsity-inducing penalization, SparScape is able to select a small subset of DBFs with enriched BSs in a set of DNA sequences from a much larger candidate set. This substantially reduces the false positives in prediction of BSs. Analysis of ChIP-Seq data in mouse embryonic stem cells and simulated data show that SparScape dramatically outperforms the naive motif scanning method and the comparable computational approaches in terms of DBF identification and BS prediction. AVAILABILITY AND IMPLEMENTATION SparScape is implemented in C++ with OpenMP (optional at compilation) and is freely available at 'www.stat.ucla.edu/∼zhou/Software.html' for academic use.
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Affiliation(s)
- Matthew Levinson
- Department of Statistics, University of California, Los Angeles, CA 90095, USA
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62
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SNAIL and miR-34a feed-forward regulation of ZNF281/ZBP99 promotes epithelial-mesenchymal transition. EMBO J 2013; 32:3079-95. [PMID: 24185900 DOI: 10.1038/emboj.2013.236] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/07/2013] [Indexed: 01/12/2023] Open
Abstract
Here, we show that expression of ZNF281/ZBP-99 is controlled by SNAIL and miR-34a/b/c in a coherent feed-forward loop: the epithelial-mesenchymal transition (EMT) inducing factor SNAIL directly induces ZNF281 transcription and represses miR-34a/b/c, thereby alleviating ZNF281 mRNA from direct down-regulation by miR-34. Furthermore, p53 activation resulted in a miR-34a-dependent repression of ZNF281. Ectopic ZNF281 expression in colorectal cancer (CRC) cells induced EMT by directly activating SNAIL, and was associated with increased migration/invasion and enhanced β-catenin activity. Furthermore, ZNF281 induced the stemness markers LGR5 and CD133, and increased sphere formation. Conversely, experimental down-regulation of ZNF281 resulted in mesenchymal-epithelial transition (MET) and inhibition of migration/invasion, sphere formation and lung metastases in mice. Ectopic c-MYC induced ZNF281 protein expression in a SNAIL-dependent manner. Experimental inactivation of ZNF281 prevented EMT induced by c-MYC or SNAIL. In primary CRC samples, expression of ZNF281 increased during tumour progression and correlated with recurrence. Taken together, these results identify ZNF281 as a component of EMT-regulating networks, which contribute to metastasis formation in CRC.
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63
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Pucci F, Gardano L, Harrington L. Short telomeres in ESCs lead to unstable differentiation. Cell Stem Cell 2013; 12:479-86. [PMID: 23561444 PMCID: PMC3629568 DOI: 10.1016/j.stem.2013.01.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/24/2012] [Accepted: 01/28/2013] [Indexed: 12/18/2022]
Abstract
Functional telomeres are critical for stem cell proliferation; however, whether they are equally important for the stability of stem cell differentiation is not known. We found that mouse embryonic stem cells (ESCs) with critically short telomeres (Tert(-/-) ESCs) initiated normal differentiation after leukemia inhibitory factor (LIF) withdrawal but, unlike control ESCs, failed to maintain stable differentiation when LIF was reintroduced to the growth medium. Tert(-/-) ESCs expressed higher levels of Nanog and, overall, had decreased genomic CpG methylation levels, which included the promoters of Oct4 and Nanog. This unstable differentiation phenotype could be rescued by telomere elongation via reintroduction of Tert, via suppression of Nanog by small hairpin RNA (shRNA) knockdown, or via enforced expression of the de novo DNA methyltransferase 3b. These results demonstrate an unexpected role of functional telomeres in the genome-wide epigenetic regulation of cell differentiation and suggest a potentially important role of telomere instability in cell fate during development or disease.
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Affiliation(s)
- Fabio Pucci
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, Michael Swann Building, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
| | - Laura Gardano
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, Michael Swann Building, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
| | - Lea Harrington
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, Michael Swann Building, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
- Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, 2950 Chemin de Polytechnique, Pavillon Marcelle-Coutu, Montréal, Québec H3T 1J4, Canada
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64
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Navarro P, Festuccia N, Colby D, Gagliardi A, Mullin NP, Zhang W, Karwacki-Neisius V, Osorno R, Kelly D, Robertson M, Chambers I. OCT4/SOX2-independent Nanog autorepression modulates heterogeneous Nanog gene expression in mouse ES cells. EMBO J 2012; 31:4547-62. [PMID: 23178592 PMCID: PMC3545296 DOI: 10.1038/emboj.2012.321] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/09/2012] [Indexed: 12/19/2022] Open
Abstract
NANOG, OCT4 and SOX2 form the core network of transcription factors supporting embryonic stem (ES) cell self-renewal. While OCT4 and SOX2 expression is relatively uniform, ES cells fluctuate between states of high NANOG expression possessing high self-renewal efficiency, and low NANOG expression exhibiting increased differentiation propensity. NANOG, OCT4 and SOX2 are currently considered to activate transcription of each of the three genes, an architecture that cannot readily account for NANOG heterogeneity. Here, we examine the architecture of the Nanog-centred network using inducible NANOG gain- and loss-of-function approaches. Rather than activating itself, Nanog activity is autorepressive and OCT4/SOX2-independent. Moreover, the influence of Nanog on Oct4 and Sox2 expression is minimal. Using Nanog:GFP reporters, we show that Nanog autorepression is a major regulator of Nanog transcription switching. We conclude that the architecture of the pluripotency gene regulatory network encodes the capacity to generate reversible states of Nanog transcription via a Nanog-centred autorepressive loop. Therefore, cellular variability in self-renewal efficiency is an emergent property of the pluripotency gene regulatory network.
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Affiliation(s)
- Pablo Navarro
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Nicola Festuccia
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Douglas Colby
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Alessia Gagliardi
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Nicholas P Mullin
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Wensheng Zhang
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Violetta Karwacki-Neisius
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Rodrigo Osorno
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - David Kelly
- Centre Optical Instrumentation Laboratory, Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Morag Robertson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
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Zfp281 mediates Nanog autorepression through recruitment of the NuRD complex and inhibits somatic cell reprogramming. Proc Natl Acad Sci U S A 2012; 109:16202-7. [PMID: 22988117 DOI: 10.1073/pnas.1208533109] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The homeodomain transcription factor Nanog plays an important role in embryonic stem cell (ESC) self-renewal and is essential for acquiring ground-state pluripotency during reprogramming. Understanding how Nanog is transcriptionally regulated is important for further dissecting mechanisms of ESC pluripotency and somatic cell reprogramming. Here, we report that Nanog is subjected to a negative autoregulatory mechanism, i.e., autorepression, in ESCs, and that such autorepression requires the coordinated action of the Nanog partner and transcriptional repressor Zfp281. Mechanistically, Zfp281 recruits the NuRD repressor complex onto the Nanog locus and maintains its integrity to mediate Nanog autorepression and, functionally, Zfp281-mediated Nanog autorepression presents a roadblock to efficient somatic cell reprogramming. Our results identify a unique transcriptional regulatory mode of Nanog gene expression and shed light into the mechanistic understanding of Nanog function in pluripotency and reprogramming.
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Das S, Jena S, Kim EM, Zavazava N, Levasseur DN. Transcriptional Regulation of Human NANOG by Alternate Promoters in Embryonic Stem Cells. JOURNAL OF STEM CELL RESEARCH & THERAPY 2012; Suppl 10:009. [PMID: 25077040 PMCID: PMC4112544 DOI: 10.4172/2157-7633.s10-009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
INTRODUCTION The potential of pluripotent stem cells to be used for cell therapy depends on a comprehensive understanding of the molecular mechanisms underlying their unique ability to specify cells of all germ layers while undergoing unlimited self-renewal. Alternative splicing and alternate promoter selection contribute to this mechanism by increasing the number of transcripts generated from a single gene locus and thus enabling expression of novel protein variants which may differ in their biological role. The homeodomain-containing transcription factor NANOG plays a critical role in maintaining the pluripotency of Embryonic Stem Cells (ESC). Therefore, a thorough understanding of the transcriptional regulation of the NANOG locus in ESCs is necessary. METHODS Regulatory footprints and transcription levels were identified for NANOG in human embryonic stem cells from data obtained using high-throughput sequencing methodologies. Quantitative real-time PCR following reverse transcription of RNA extracted human ESCs was used to validate the expression of transcripts from a region that extends upstream of the annotated NANOG transcriptional start. Promoter identification and characterization were performed using promoter reporter and electrophoretic mobility shift assays. RESULTS Transcriptionally active chromatin marking and transcription factor binding site enrichment were observed at a region upstream of the known transcriptional start site of NANOG. Expression of novel transcripts from this transcriptionally active region confirmed the existence of NANOG alternative splicing in human ESCs. We identified an alternate NANOG promoter of significant strength at this upstream region. We also discovered that NANOG autoregulates its expression by binding to its proximal downstream promoter. CONCLUSION Our study reveals novel transcript expression from NANOG in human ESCs, indicating that alternative splicing increases the diversity of transcripts originating from the NANOG locus and that these transcripts are expressed by an alternate promoter. Alternative splicing and alternate promoter usage collaborate to regulate NANOG, enabling its function in the maintenance of ESCs.
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Affiliation(s)
- Satyabrata Das
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, Iowa City, USA
| | - Snehalata Jena
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, Iowa City, USA
| | - Eun-Mi Kim
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, Iowa City, USA
| | - Nicholas Zavazava
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, Iowa City, USA
| | - Dana N. Levasseur
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, Iowa City, USA
- Programs in Genetics and Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa 52242, USA
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Gower-Winter SD, Levenson CW. Zinc in the central nervous system: From molecules to behavior. Biofactors 2012; 38:186-93. [PMID: 22473811 PMCID: PMC3757551 DOI: 10.1002/biof.1012] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 03/08/2012] [Indexed: 01/28/2023]
Abstract
The trace metal zinc is a biofactor that plays essential roles in the central nervous system across the lifespan from early neonatal brain development through the maintenance of brain function in adults. At the molecular level, zinc regulates gene expression through transcription factor activity and is responsible for the activity of dozens of key enzymes in neuronal metabolism. At the cellular level, zinc is a modulator of synaptic activity and neuronal plasticity in both development and adulthood. Given these key roles, it is not surprising that alterations in brain zinc status have been implicated in a wide array of neurological disorders including impaired brain development, neurodegenerative disorders such as Alzheimer's disease, and mood disorders including depression. Zinc has also been implicated in neuronal damage associated with traumatic brain injury, stroke, and seizure. Understanding the mechanisms that control brain zinc homeostasis is thus critical to the development of preventive and treatment strategies for these and other neurological disorders.
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Affiliation(s)
- Shannon D. Gower-Winter
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, FL, USA
| | - Cathy W. Levenson
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, FL, USA
- Program in Neuroscience, Florida State University, College of Medicine, Tallahassee, FL, USA
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Neff AT, Lee JY, Wilusz J, Tian B, Wilusz CJ. Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells. Genome Res 2012; 22:1457-67. [PMID: 22534399 PMCID: PMC3409259 DOI: 10.1101/gr.134312.111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pluripotency is a unique state in which cells can self-renew indefinitely but also retain the ability to differentiate into other cell types upon receipt of extracellular cues. Although it is clear that stem cells have a distinct transcriptional program, little is known about how alterations in post-transcriptional mechanisms, such as mRNA turnover, contribute to the achievement and maintenance of pluripotency. Here we have assessed the rates of decay for the majority of mRNAs expressed in induced pluripotent stem (iPS) cells and the fully differentiated human foreskin fibroblasts (HFFs) they were derived from. Comparison of decay rates in the two cell types led to the discovery of three independent regulatory mechanisms that allow coordinated turnover of specific groups of mRNAs. One mechanism results in increased stability of many histone mRNAs in iPS cells. A second pathway stabilizes a large set of zinc finger protein mRNAs, potentially through reduced levels of miRNAs that target them. Finally, a group of transcripts bearing 3' UTR C-rich sequence elements, many of which encode transcription factors, are significantly less stable in iPS cells. Intriguingly, two poly(C)-binding proteins that recognize this type of element are reciprocally expressed in iPS and HFF cells. Overall, our results highlight the importance of post-transcriptional control in pluripotent cells and identify miRNAs and RNA-binding proteins whose activity may coordinately control expression of a wide range of genes in iPS cells.
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Affiliation(s)
- Ashley T Neff
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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