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Tsaytler P, Blaess G, Scholze-Wittler M, Koch F, Herrmann BG. Early neural specification of stem cells is mediated by a set of SOX2-dependent neural-associated enhancers. Stem Cell Reports 2024; 19:618-628. [PMID: 38579708 PMCID: PMC11103784 DOI: 10.1016/j.stemcr.2024.03.003] [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: 08/21/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024] Open
Abstract
SOX2 is a transcription factor involved in the regulatory network maintaining the pluripotency of embryonic stem cells in culture as well as in early embryos. In addition, SOX2 plays a pivotal role in neural stem cell formation and neurogenesis. How SOX2 can serve both processes has remained elusive. Here, we identified a set of SOX2-dependent neural-associated enhancers required for neural lineage priming. They form a distinct subgroup (1,898) among 8,531 OCT4/SOX2/NANOG-bound enhancers characterized by enhanced SOX2 binding and chromatin accessibility. Activation of these enhancers is triggered by neural induction of wild-type cells or by default in Smad4-ablated cells resistant to mesoderm induction and is antagonized by mesodermal transcription factors via Sox2 repression. Our data provide mechanistic insight into the transition from the pluripotency state to the early neural fate and into the regulation of early neural versus mesodermal specification in embryonic stem cells and embryos.
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Affiliation(s)
- Pavel Tsaytler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| | - Gaby Blaess
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Manuela Scholze-Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Frederic Koch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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2
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Skardžiūtė K, Kvederavičiūtė K, Pečiulienė I, Narmontė M, Gibas P, Ličytė J, Klimašauskas S, Kriukienė E. One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci. Cell Chem Biol 2024; 31:607-621.e9. [PMID: 38154461 PMCID: PMC10962225 DOI: 10.1016/j.chembiol.2023.12.003] [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: 06/26/2023] [Revised: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
We present a method, named Mx-TOP, for profiling of three epigenetic regulatory layers-chromatin accessibility, general DNA modification, and DNA hydroxymethylation-from a single library. The approach is based on chemo-enzymatic covalent tagging of unmodified CG sites and hydroxymethylated cytosine (5hmC) along with GC sites in chromatin, which are then mapped using tag-selective base-resolution TOP-seq sequencing. Our in-depth validation of the approach revealed its sensitivity and informativity in evaluating chromatin accessibility and DNA modification interactions that drive transcriptional regulation. We employed the technology in a study of chromatin and DNA demethylation dynamics during in vitro neuronal differentiation. The study highlighted the involvement of gene body 5hmC in modulating an extensive decoupling between promoter accessibility and transcription. The importance of 5hmC in chromatin remodeling was further demonstrated by the observed resistance of the developmentally acquired open loci to the global 5hmC erasure in neuronal progenitors.
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Affiliation(s)
- Kotryna Skardžiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Inga Pečiulienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Milda Narmontė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania.
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3
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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4
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Ong ALC, Kokaji T, Kishi A, Takihara Y, Shinozuka T, Shimamoto R, Isotani A, Shirai M, Sasai N. Acquisition of neural fate by combination of BMP blockade and chromatin modification. iScience 2023; 26:107887. [PMID: 37771660 PMCID: PMC10522999 DOI: 10.1016/j.isci.2023.107887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/07/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
Neural induction is a process where naive cells are converted into committed cells with neural characteristics, and it occurs at the earliest step during embryogenesis. Although the signaling molecules and chromatin remodeling for neural induction have been identified, the mutual relationships between these molecules are yet to be fully understood. By taking advantage of the neural differentiation system of mouse embryonic stem (ES) cells, we discovered that the BMP signal regulates the expression of several polycomb repressor complex (PRC) component genes. We particularly focused on Polyhomeotic Homolog 1 (Phc1) and established Phc1-knockout (Phc1-KO) ES cells. We found that Phc1-KO failed to acquire the neural fate, and the cells remained in pluripotent or primitive non-neural states. Chromatin accessibility analysis suggests that Phc1 is essential for chromatin packing. Aberrant upregulation of the BMP signal was confirmed in the Phc1 homozygotic mutant embryos. Taken together, Phc1 is required for neural differentiation through epigenetic modification.
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Affiliation(s)
- Agnes Lee Chen Ong
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Toshiya Kokaji
- Data-driven biology, NAIST Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Arisa Kishi
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Yoshihiro Takihara
- Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Takuma Shinozuka
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ren Shimamoto
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Manabu Shirai
- Omics Research Center (ORC), National Cerebral and Cardiovascular Center, 6-1 Kishibe Shinmachi, Suita, Osaka 564-8565, Japan
| | - Noriaki Sasai
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
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5
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Petrović DJ, Jagečić D, Krasić J, Sinčić N, Mitrečić D. Effect of Fetal Bovine Serum or Basic Fibroblast Growth Factor on Cell Survival and the Proliferation of Neural Stem Cells: The Influence of Homocysteine Treatment. Int J Mol Sci 2023; 24:14161. [PMID: 37762465 PMCID: PMC10531752 DOI: 10.3390/ijms241814161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
In vitro cell culture is a routinely used method which is also applied for in vitro modeling of various neurological diseases. On the other hand, media used for cell culture are often not strictly standardized between laboratories, which hinders the comparison of the obtained results. Here, we compared the effects of homocysteine (Hcy), a molecule involved in neurodegeneration, on immature cells of the nervous system cultivated in basal medium or media supplemented by either fetal bovine serum or basic fibroblast growth factor. The number of cells in basal media supplemented with basic fibroblast growth factor (bFGF) was 2.5 times higher in comparison to the number of cells in basal media supplemented with fetal bovine serum (FBS). We also found that the neuron-specific β-3-tubulin protein expression dose dependently decreased with increasing Hcy exposure. Interestingly, bFGF exerts a protective effect on β-3-tubulin protein expression at a concentration of 1000 µM Hcy compared to FBS-treated neural stem cells on Day 7. Supplementation with bFGF increased SOX2 protein expression two-fold compared to FBS supplementation. GFAP protein expression increased five-fold on Day 3 in FBS-treated neural stem cells, whereas on Day 7, bFGF increased GFAP expression two-fold compared to FBS-treated neural stem cells. Here, we have clearly shown that the selection of culturing media significantly influences various cellular parameters, which, in turn, can lead to different conclusions in experiments based on in vitro models of pathological conditions.
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Affiliation(s)
- Dražen Juraj Petrović
- Laboratory for Stem Cells, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia; (D.J.P.); (D.J.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Glycoscience Research Laboratory, Genos Ltd., 10000 Zagreb, Croatia
- BIMIS—Biomedical Research Center Šalata, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Denis Jagečić
- Laboratory for Stem Cells, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia; (D.J.P.); (D.J.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- BIMIS—Biomedical Research Center Šalata, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Jure Krasić
- Laboratory for Stem Cells, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia; (D.J.P.); (D.J.)
- BIMIS—Biomedical Research Center Šalata, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Laboratory for Neurogenomics and In Situ Hybridization, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Nino Sinčić
- BIMIS—Biomedical Research Center Šalata, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers (epiMark), Department of Medical Biology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Dinko Mitrečić
- Laboratory for Stem Cells, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia; (D.J.P.); (D.J.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- BIMIS—Biomedical Research Center Šalata, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
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6
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Reza E, Azizi H, Skutella T. Sox2 Localization During Spermatogenesis and Its Association with other Spermatogenesis Markers Using Protein-Protein Network Analysis. J Reprod Infertil 2023; 24:171-180. [PMID: 37663428 PMCID: PMC10471949 DOI: 10.18502/jri.v24i3.13273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/07/2023] [Indexed: 09/05/2023] Open
Abstract
Background Sox2 (SRY box2) is an essential transcription factor that plays a vital role in spermatogenesis and regulates the genes in this process. Sox2 is important for pluripotency, self-renewal, and even spermatogonial stem cell differentiation. This gene is found in pluripotent and specialized cells, and it is involved in their biological activities. Methods Protein-protein interaction (PPI) network analysis was performed during spermatogenesis using NCBI, STRING, and Cytoscape databases. Then, after isolating spermatogonial stem cells from 6 C57BL/6 mice, mouse embryonic stem cells and ES-like cells were prepared. In the following, Sox2 expression was examined in differentiated and undifferentiated spermatogonia by immunohistochemistry (IMH), immunocytochemistry (ICC), and Fluidigm PCR (polymerase chain reaction). Finally, the results were compared using the Kruskal-Wallis and Dunn tests at the significance level of p<0.05. Results The results of this experiment showed that contrary to expectations, Sox2 has cytoplasmic expression in undifferentiated cells and nuclear expression in differentiated cells in in vitro conditions. In addition, the expression of Sox2 increased during differentiation. Fluidigm PCR showed a significantly higher expression of Sox2 (p<0.05) in differentiated compared to undifferentiated spermatogonia. Sox2 has an interaction with other genes during spermatogenesis such as Oct4, Nanog, Klf4, Stra8, Smad1, Tcf3, and Osm. Conclusion Sox2, which is known as a pluripotency marker, has a vital role in spermatogenesis and could be a differential marker. Sox2 has strong connections with other genes such as Oct4, Nanog, Klf4, Tcf3, Osm, Stra8, Lim2, Smad1, Gdnf, and Kit.
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Affiliation(s)
- Emad Reza
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Thomas Skutella
- Institute for Anatomy and Cell Biology, Medical Faculty, University of Heidelberg, Heidelberg, Germany
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7
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Kamal A, Arnold C, Claringbould A, Moussa R, Servaas NH, Kholmatov M, Daga N, Nogina D, Mueller‐Dott S, Reyes‐Palomares A, Palla G, Sigalova O, Bunina D, Pabst C, Zaugg JB. GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks. Mol Syst Biol 2023; 19:e11627. [PMID: 37073532 PMCID: PMC10258561 DOI: 10.15252/msb.202311627] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023] Open
Abstract
Enhancers play a vital role in gene regulation and are critical in mediating the impact of noncoding genetic variants associated with complex traits. Enhancer activity is a cell-type-specific process regulated by transcription factors (TFs), epigenetic mechanisms and genetic variants. Despite the strong mechanistic link between TFs and enhancers, we currently lack a framework for jointly analysing them in cell-type-specific gene regulatory networks (GRN). Equally important, we lack an unbiased way of assessing the biological significance of inferred GRNs since no complete ground truth exists. To address these gaps, we present GRaNIE (Gene Regulatory Network Inference including Enhancers) and GRaNPA (Gene Regulatory Network Performance Analysis). GRaNIE (https://git.embl.de/grp-zaugg/GRaNIE) builds enhancer-mediated GRNs based on covariation of chromatin accessibility and RNA-seq across samples (e.g. individuals), while GRaNPA (https://git.embl.de/grp-zaugg/GRaNPA) assesses the performance of GRNs for predicting cell-type-specific differential expression. We demonstrate their power by investigating gene regulatory mechanisms underlying the response of macrophages to infection, cancer and common genetic traits including autoimmune diseases. Finally, our methods identify the TF PURA as a putative regulator of pro-inflammatory macrophage polarisation.
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Affiliation(s)
- Aryan Kamal
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Annique Claringbould
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Rim Moussa
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Nila H Servaas
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Maksim Kholmatov
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Neha Daga
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Daria Nogina
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Sophia Mueller‐Dott
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Armando Reyes‐Palomares
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Present address:
Department of Biochemistry and Molecular BiologyComplutense University of MadridMadridSpain
| | - Giovanni Palla
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Present address:
Institute of Computational BiologyHelmholtz Center MunichOberschleißheimGermany
| | - Olga Sigalova
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
| | - Daria Bunina
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Caroline Pabst
- Department of Medicine V, Hematology, Oncology and RheumatologyUniversity Hospital HeidelbergHeidelbergGermany
- Molecular Medicine Partnership UnitUniversity of HeidelbergHeidelbergGermany
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Molecular Medicine Partnership UnitUniversity of HeidelbergHeidelbergGermany
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8
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Sullivan AE. Epigenetic Control of Cell Potency and Fate Determination during Mammalian Gastrulation. Genes (Basel) 2023; 14:1143. [PMID: 37372324 DOI: 10.3390/genes14061143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Pluripotent embryonic stem cells have a unique and characteristic epigenetic profile, which is critical for differentiation to all embryonic germ lineages. When stem cells exit the pluripotent state and commit to lineage-specific identities during the process of gastrulation in early embryogenesis, extensive epigenetic remodelling mediates both the switch in cellular programme and the loss of potential to adopt alternative lineage programmes. However, it remains to be understood how the stem cell epigenetic profile encodes pluripotency, or how dynamic epigenetic regulation helps to direct cell fate specification. Recent advances in stem cell culture techniques, cellular reprogramming, and single-cell technologies that can quantitatively profile epigenetic marks have led to significant insights into these questions, which are important for understanding both embryonic development and cell fate engineering. This review provides an overview of key concepts and highlights exciting new advances in the field.
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Affiliation(s)
- Adrienne E Sullivan
- Quantitative Stem Cell Biology Lab, Francis Crick Institute, London NW1 1AT, UK
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
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9
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Copeland J, Merkuri F, Simoes-Costa M. ChIP-Seq Protocol for In Vitro Cell Differentiation Systems. Methods Mol Biol 2023; 2599:49-58. [PMID: 36427142 DOI: 10.1007/978-1-0716-2847-8_5] [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] [Indexed: 06/16/2023]
Abstract
In vitro differentiation systems provide a flexible platform for understanding complex developmental processes. Here, we provide a comprehensive protocol for the preparation and analysis of ChIP-seq libraries for human-induced neural crest cells (hiNCCs) from human embryonic stem cells (hESCs). This workflow is aimed at identifying interactions between transcription factors and cis regulatory elements, which serve as useful assays in uncovering gene regulatory principles during development.
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Affiliation(s)
- Jacqueline Copeland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Fjodor Merkuri
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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10
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Current challenges in understanding the role of enhancers in disease. Nat Struct Mol Biol 2022; 29:1148-1158. [PMID: 36482255 DOI: 10.1038/s41594-022-00896-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
Abstract
Enhancers play a central role in the spatiotemporal control of gene expression and tend to work in a cell-type-specific manner. In addition, they are suggested to be major contributors to phenotypic variation, evolution and disease. There is growing evidence that enhancer dysfunction due to genetic, structural or epigenetic mechanisms contributes to a broad range of human diseases referred to as enhanceropathies. Such mechanisms often underlie the susceptibility to common diseases, but can also play a direct causal role in cancer or Mendelian diseases. Despite the recent gain of insights into enhancer biology and function, we still have a limited ability to predict how enhancer dysfunction impacts gene expression. Here we discuss the major challenges that need to be overcome when studying the role of enhancers in disease etiology and highlight opportunities and directions for future studies, aiming to disentangle the molecular basis of enhanceropathies.
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11
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Hovland AS, Bhattacharya D, Azambuja AP, Pramio D, Copeland J, Rothstein M, Simoes-Costa M. Pluripotency factors are repurposed to shape the epigenomic landscape of neural crest cells. Dev Cell 2022; 57:2257-2272.e5. [PMID: 36182685 PMCID: PMC9743141 DOI: 10.1016/j.devcel.2022.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/28/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
Yamanaka factors are essential for establishing pluripotency in embryonic stem cells, but their function in multipotent stem cell populations is poorly understood. Here, we show that OCT4 and SOX2 cooperate with tissue-specific transcription factors to promote neural crest formation. By assessing avian and human neural crest cells at distinct developmental stages, we characterized the epigenomic changes that occur during their specification, migration, and early differentiation. This analysis determined that the OCT4-SOX2 dimer is required to establish a neural crest epigenomic signature that is lost upon cell fate commitment. The OCT4-SOX2 genomic targets in the neural crest differ from those of embryonic stem cells, indicating the dimer displays context-specific functions. Binding of OCT4-SOX2 to neural crest enhancers requires pioneer factor TFAP2A, which physically interacts with the dimer to modify its genomic targets. Our results demonstrate how Yamanaka factors are repurposed in multipotent cells to control chromatin organization and define their developmental potential.
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Affiliation(s)
- Austin S Hovland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | | | - Ana Paula Azambuja
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dimitrius Pramio
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jacqueline Copeland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Megan Rothstein
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA.
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12
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Emerging Roles of TRIM Family Proteins in Gliomas Pathogenesis. Cancers (Basel) 2022; 14:cancers14184536. [PMID: 36139694 PMCID: PMC9496762 DOI: 10.3390/cancers14184536] [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: 08/10/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Simple Summary Gliomas remain challenging tumors due to their increased heterogeneity, complex molecular profile, and infiltrative phenotype that are often associated with a dismal prognosis. In a constant search for molecular changes and associated mechanisms, the TRIM protein family has emerged as an important area of investigation because of the regulation of vital cellular processes involved in brain pathophysiology that may possibly lead to brain tumor development. Herein, we discuss the diverse role of TRIM proteins in glioma progression, aiming to detect potential targets for future intervention. Abstract Gliomas encompass a vast category of CNS tumors affecting both adults and children. Treatment and diagnosis are often impeded due to intratumor heterogeneity and the aggressive nature of the more malignant forms. It is therefore essential to elucidate the molecular mechanisms and explore the intracellular signaling pathways underlying tumor pathology to provide more promising diagnostic, prognostic, and therapeutic tools for gliomas. The tripartite motif-containing (TRIM) superfamily of proteins plays a key role in many physiological cellular processes, including brain development and function. Emerging evidence supports the association of TRIMs with a wide variety of cancers, exhibiting both an oncogenic as well as a tumor suppressive role depending on cancer type. In this review, we provide evidence of the pivotal role of TRIM proteins in gliomagenesis and exploit their potential as prognostic biomarkers and therapeutic targets.
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Liang X, Brooks MJ, Swaroop A. Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina. Hum Mol Genet 2022; 31:3914-3933. [PMID: 35776116 DOI: 10.1093/hmg/ddac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/12/2022] Open
Abstract
The basic motif-leucine zipper (bZIP) transcription factor NRL determines rod photoreceptor cell fate during retinal development, and its loss leads to cone-only retina in mice. NRL works synergistically with homeodomain protein CRX and other regulatory factors to control the transcription of most genes associated with rod morphogenesis and functional maturation, which span over a period of several weeks in the mammalian retina. We predicted that NRL gradually establishes rod cell identity and function by temporal and dynamic regulation of stage-specific transcriptional targets. Therefore, we mapped the genomic occupancy of NRL at four stages of mouse photoreceptor differentiation by CUT&RUN analysis. Dynamics of NRL-binding revealed concordance with the corresponding changes in transcriptome of the developing rods. Notably, we identified c-Jun proto-oncogene as one of the targets of NRL, which could bind to specific cis-elements in the c-Jun promoter and modulate its activity in HEK293 cells. Coimmunoprecipitation studies showed association of NRL with c-Jun, also a bZIP protein, in transfected cells as well as in developing mouse retina. Additionally, shRNA-mediated knockdown of c-Jun in the mouse retina in vivo resulted in altered expression of almost 1000 genes, with reduced expression of phototransduction genes and many direct targets of NRL in rod photoreceptors. We propose that c-Jun-NRL heterodimers prime the NRL-directed transcriptional program in neonatal rod photoreceptors before high NRL expression suppresses c-Jun at later stages. Our study highlights a broader cooperation among cell-type restricted and widely expressed bZIP proteins, such as c-Jun, in specific spatiotemporal contexts during cellular differentiation.
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Affiliation(s)
- Xulong Liang
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Matthew J Brooks
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
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14
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Fotuhi Siahpirani A, Knaack S, Chasman D, Seirup M, Sridharan R, Stewart R, Thomson J, Roy S. Dynamic regulatory module networks for inference of cell type-specific transcriptional networks. Genome Res 2022; 32:1367-1384. [PMID: 35705328 PMCID: PMC9341506 DOI: 10.1101/gr.276542.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
Changes in transcriptional regulatory networks can significantly alter cell fate. To gain insight into transcriptional dynamics, several studies have profiled bulk multi-omic data sets with parallel transcriptomic and epigenomic measurements at different stages of a developmental process. However, integrating these data to infer cell type–specific regulatory networks is a major challenge. We present dynamic regulatory module networks (DRMNs), a novel approach to infer cell type–specific cis-regulatory networks and their dynamics. DRMN integrates expression, chromatin state, and accessibility to predict cis-regulators of context-specific expression, where context can be cell type, developmental stage, or time point, and uses multitask learning to capture network dynamics across linearly and hierarchically related contexts. We applied DRMNs to study regulatory network dynamics in three developmental processes, each showing different temporal relationships and measuring a different combination of regulatory genomic data sets: cellular reprogramming, liver dedifferentiation, and forward differentiation. DRMN identified known and novel regulators driving cell type–specific expression patterns, showing its broad applicability to examine dynamics of gene regulatory networks from linearly and hierarchically related multi-omic data sets.
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Affiliation(s)
| | - Sara Knaack
- Wisconsin Institute for Discovery, University of Wisconsin-Madison
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison
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15
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Lenz J, Konecna P, Tichy F, Machacova D, Fiala L, Hurnik P, Kyllar M. Unique expression patterns of the embryonal stem cell marker SOX2 and hormone receptors suggest the existence of a subpopulation of epithelial stem/progenitor cells in porcine and bovine endometrium. Vet Med Sci 2022; 8:1489-1501. [PMID: 35561288 PMCID: PMC9297784 DOI: 10.1002/vms3.802] [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] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND There are currently insufficient data on the population of endometrial epithelial stem/progenitor cells in farm animals. OBJECTIVES With the aim of identifying a potential population of epithelial stem/progenitor cells in the porcine and bovine endometrium, this study immunohistochemically examined the expression patterns of the oestrogen and progesterone receptors, as well as that of the embryonal stem cell marker SOX2. METHODS A total of 24 endometrial tissue samples obtained from cycling pigs (n = 12) and cows (n = 12) were included in our study. Each endometrium was divided into basal, middle and luminal portions. The percentage of marker-positive cells and the intensity of the immunoreaction in each portion of the endometrium were determined. RESULTS Inverse expression patterns of SOX2 and progesterone receptors were found in both animal species throughout the oestrous cycle. Strong diffuse SOX2 expression was detected in the basal portions of the glands, while a significant decrease in positivity and a weak immunoreaction were found in the luminal two thirds of the glandular epithelium. Strong progesterone receptor expression was observed in at least 90% of glandular cells in the middle and luminal portions, whereas weak staining and significant decrease in positivity were detected in the basal portions of the glands. One oestrogen receptor expression pattern resembled that of progesterone receptors. CONCLUSION The inverse expression patterns of SOX2 and hormone (especially progesterone) receptors suggest that endometrial epithelial stem/progenitor cells represent a subset of cells that reside in the basal portions of the endometrial glands in both the bovine and porcine endometrium.
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Affiliation(s)
- Jiri Lenz
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic.,Department of Pathology, Znojmo Hospital, Znojmo, Czech Republic.,Cytohisto s.r.o., Břeclav, Czech Republic
| | - Petra Konecna
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Frantisek Tichy
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Dominika Machacova
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ludek Fiala
- Cytohisto s.r.o., Břeclav, Czech Republic.,Department of Sexology, Psychiatric Clinic, Faculty of Medicine, Charles University Pilsen, Pilsen, Czech Republic.,Institute of Sexology, First Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | | | - Michal Kyllar
- Department of Pathobiology, Institute of Morphology, University of Veterinary Medicine Vienna, Vienna, Austria
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16
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Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders. Nat Commun 2021; 12:6469. [PMID: 34753942 PMCID: PMC8578637 DOI: 10.1038/s41467-021-26810-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/21/2021] [Indexed: 01/06/2023] Open
Abstract
Subunit switches in the BAF chromatin remodeler are essential during development. ARID1B and its paralog ARID1A encode for mutually exclusive BAF subunits. De novo ARID1B haploinsufficient mutations cause neurodevelopmental disorders, including Coffin-Siris syndrome, which is characterized by neurological and craniofacial features. Here, we leveraged ARID1B+/− Coffin-Siris patient-derived iPSCs and modeled cranial neural crest cell (CNCC) formation. We discovered that ARID1B is active only during the first stage of this process, coinciding with neuroectoderm specification, where it is part of a lineage-specific BAF configuration (ARID1B-BAF). ARID1B-BAF regulates exit from pluripotency and lineage commitment by attenuating thousands of enhancers and genes of the NANOG and SOX2 networks. In iPSCs, these enhancers are maintained active by ARID1A-containing BAF. At the onset of differentiation, cells transition from ARID1A- to ARID1B-BAF, eliciting attenuation of the NANOG/SOX2 networks and triggering pluripotency exit. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at the pluripotency enhancers throughout all stages of CNCC formation. This leads to persistent NANOG/SOX2 activity which impairs CNCC formation. Despite showing the typical neural crest signature (TFAP2A/SOX9-positive), ARID1B-haploinsufficient CNCCs are also aberrantly NANOG-positive. These findings suggest a connection between ARID1B mutations, neuroectoderm specification and a pathogenic mechanism for Coffin-Siris syndrome. Mutations in the ARID1B subunit of the BAF chromatin remodeling complex are associated with the neurodevelopmental Coffin-Siris syndrome. Here the authors reveal that there is a transition from ARID1A-containing complexes to ARID1B during cranial neural crest cell differentiation that is impaired in Coffin-Siris patient-derived cells, which is important for exit from pluripotency.
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17
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Weidemüller P, Kholmatov M, Petsalaki E, Zaugg JB. Transcription factors: Bridge between cell signaling and gene regulation. Proteomics 2021; 21:e2000034. [PMID: 34314098 DOI: 10.1002/pmic.202000034] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 01/17/2023]
Abstract
Transcription factors (TFs) are key regulators of intrinsic cellular processes, such as differentiation and development, and of the cellular response to external perturbation through signaling pathways. In this review we focus on the role of TFs as a link between signaling pathways and gene regulation. Cell signaling tends to result in the modulation of a set of TFs that then lead to changes in the cell's transcriptional program. We highlight the molecular layers at which TF activity can be measured and the associated technical and conceptual challenges. These layers include post-translational modifications (PTMs) of the TF, regulation of TF binding to DNA through chromatin accessibility and epigenetics, and expression of target genes. We highlight that a large number of TFs are understudied in both signaling and gene regulation studies, and that our knowledge about known TF targets has a strong literature bias. We argue that TFs serve as a perfect bridge between the fields of gene regulation and signaling, and that separating these fields hinders our understanding of cell functions. Multi-omics approaches that measure multiple dimensions of TF activity are ideally suited to study the interplay of cell signaling and gene regulation using TFs as the anchor to link the two fields.
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Affiliation(s)
- Paula Weidemüller
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Maksim Kholmatov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Evangelia Petsalaki
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg, 69117, Germany
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18
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Dehghani H. Regulation of Chromatin Organization in Cell Stemness: The Emerging Role of Long Non-coding RNAs. Stem Cell Rev Rep 2021; 17:2042-2053. [PMID: 34181184 DOI: 10.1007/s12015-021-10209-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 12/27/2022]
Abstract
Chromatin is organized as chromosome territories in the nucleus of an interphase cell. The cell-type- and cell-state-specific organization of chromatin including the location, volume, compaction level, and spatial arrangement of chromosome territories are the major determinants of genome function. In addition, in response to different signaling stimuli and regulatory cues, it is the dynamic adaptation of chromatin structure that establishes and organizes transcriptional programs. It is known that varying levels of stemness are defined by gene regulatory networks. Accordingly, chromatin is the main milieu to host the transcriptional programs and gene regulatory networks responsible for the stemness status of a cell. In this review, our current understanding of the spatial organization of chromatin and the ways by which it defines stemness are discussed. In particular, the role of lncRNAs that regulate and affect chromatin organization and stemness properties are delineated. These roles can be categorized into the topics of specific binding to and epigenetic regulation of the promoter of pluripotency genes, their interaction with transcription factors, coordinating the intra- and inter-chromosomal looping of pluripotency-related genes, and their RNA-independent functions. This review brings together the results of studies that have begun to clarify the emerging roles of lncRNAs in the regulation of chromatin organization adapted for stemness and cancer plasticity.
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Affiliation(s)
- Hesam Dehghani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
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19
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Sogut MS, Venugopal C, Kandemir B, Dag U, Mahendram S, Singh S, Gulfidan G, Arga KY, Yilmaz B, Kurnaz IA. ETS-Domain Transcription Factor Elk-1 Regulates Stemness Genes in Brain Tumors and CD133+ BrainTumor-Initiating Cells. J Pers Med 2021; 11:jpm11020125. [PMID: 33672811 PMCID: PMC7917801 DOI: 10.3390/jpm11020125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/22/2022] Open
Abstract
Elk-1, a member of the ternary complex factors (TCFs) within the ETS (E26 transformation-specific) domain superfamily, is a transcription factor implicated in neuroprotection, neurodegeneration, and brain tumor proliferation. Except for known targets, c-fos and egr-1, few targets of Elk-1 have been identified. Interestingly, SMN, SOD1, and PSEN1 promoters were shown to be regulated by Elk-1. On the other hand, Elk-1 was shown to regulate the CD133 gene, which is highly expressed in brain-tumor-initiating cells (BTICs) and used as a marker for separating this cancer stem cell population. In this study, we have carried out microarray analysis in SH-SY5Y cells overexpressing Elk-1-VP16, which has revealed a large number of genes significantly regulated by Elk-1 that function in nervous system development, embryonic development, pluripotency, apoptosis, survival, and proliferation. Among these, we have shown that genes related to pluripotency, such as Sox2, Nanog, and Oct4, were indeed regulated by Elk-1, and in the context of brain tumors, we further showed that Elk-1 overexpression in CD133+ BTIC population results in the upregulation of these genes. When Elk-1 expression is silenced, the expression of these stemness genes is decreased. We propose that Elk-1 is a transcription factor upstream of these genes, regulating the self-renewal of CD133+ BTICs.
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Affiliation(s)
- Melis Savasan Sogut
- Institute of Biotechnology, Gebze Technical University, 41400 Kocaeli, Turkey; (M.S.S.); (B.K.)
- Molecular Neurobiology Laboratory (AxanLab), Department of Molecular Biology and Genetics, Gebze Technical University, 41400 Kocaeli, Turkey
- Biotechnology Graduate Program, Graduate School of Sciences, Yeditepe University, 26 Agustos Yerlesimi, Kayisdagi, 34755 Istanbul, Turkey;
| | - Chitra Venugopal
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.V.); (S.M.); (S.S.)
| | - Basak Kandemir
- Institute of Biotechnology, Gebze Technical University, 41400 Kocaeli, Turkey; (M.S.S.); (B.K.)
- Molecular Neurobiology Laboratory (AxanLab), Department of Molecular Biology and Genetics, Gebze Technical University, 41400 Kocaeli, Turkey
- Biotechnology Graduate Program, Graduate School of Sciences, Yeditepe University, 26 Agustos Yerlesimi, Kayisdagi, 34755 Istanbul, Turkey;
| | - Ugur Dag
- Biotechnology Graduate Program, Graduate School of Sciences, Yeditepe University, 26 Agustos Yerlesimi, Kayisdagi, 34755 Istanbul, Turkey;
| | - Sujeivan Mahendram
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.V.); (S.M.); (S.S.)
| | - Sheila Singh
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.V.); (S.M.); (S.S.)
| | - Gizem Gulfidan
- Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey; (G.G.); (K.Y.A.)
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey; (G.G.); (K.Y.A.)
| | - Bayram Yilmaz
- Department of Physiology, Faculty of Medicine, Yeditepe University, 26 Agustos Yerlesimi, Kayisdagi, 34755 Istanbul, Turkey
- Correspondence: (B.Y.); (I.A.K.)
| | - Isil Aksan Kurnaz
- Institute of Biotechnology, Gebze Technical University, 41400 Kocaeli, Turkey; (M.S.S.); (B.K.)
- Molecular Neurobiology Laboratory (AxanLab), Department of Molecular Biology and Genetics, Gebze Technical University, 41400 Kocaeli, Turkey
- Correspondence: (B.Y.); (I.A.K.)
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20
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Lo EKW, Su EY, Cahan P. Evaluation of Bunina et al.: Synthesizing Multi-omics Data to Delineate Neuronal Differentiation. Cell Syst 2020; 10:459-460. [PMID: 32585153 DOI: 10.1016/j.cels.2020.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
One snapshot of the peer review process for "Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons" (Bunina et al., 2020).
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Affiliation(s)
- Emily K W Lo
- Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Emily Y Su
- Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Patrick Cahan
- Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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