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Zheng R, Moynahan K, Georgomanolis T, Pavlenko E, Geissen S, Mizi A, Grimm S, Nemade H, Rehimi R, Bastigkeit J, Lackmann JW, Adam M, Rada-Iglesias A, Nuernberg P, Klinke A, Poepsel S, Baldus S, Papantonis A, Kargapolova Y. Remodeling of the endothelial cell transcriptional program via paracrine and DNA-binding activities of MPO. iScience 2024; 27:108898. [PMID: 38322992 PMCID: PMC10844825 DOI: 10.1016/j.isci.2024.108898] [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: 07/04/2022] [Revised: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Myeloperoxidase (MPO) is an enzyme that functions in host defense. MPO is released into the vascular lumen by neutrophils during inflammation and may adhere and subsequently penetrate endothelial cells (ECs) coating vascular walls. We show that MPO enters the nucleus of ECs and binds chromatin independently of its enzymatic activity. MPO drives chromatin decondensation at its binding sites and enhances condensation at neighboring regions. It binds loci relevant for endothelial-to-mesenchymal transition (EndMT) and affects the migratory potential of ECs. Finally, MPO interacts with the RNA-binding factor ILF3 thereby affecting its relative abundance between cytoplasm and nucleus. This interaction leads to change in stability of ILF3-bound transcripts. MPO-knockout mice exhibit reduced number of ECs at scar sites following myocardial infarction, indicating reduced neovascularization. In summary, we describe a non-enzymatic role for MPO in coordinating EndMT and controlling the fate of endothelial cells through direct chromatin binding and association with co-factors.
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Affiliation(s)
- Ruiyuan Zheng
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Kyle Moynahan
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Theodoros Georgomanolis
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Egor Pavlenko
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Simon Geissen
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Simon Grimm
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Harshal Nemade
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Jil Bastigkeit
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Jan-Wilm Lackmann
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cluster of Excellence on Cellular Stress Responses in Age-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Matti Adam
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, 39011 Santander, Spain
| | - Peter Nuernberg
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Anna Klinke
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Simon Poepsel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Stephan Baldus
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yulia Kargapolova
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
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Siqueira E, Kim BH, Reser L, Chow R, Delaney K, Esteller M, Ross MM, Shabanowitz J, Hunt DF, Guil S, Ausió J. Analysis of the interplay between MeCP2 and histone H1 during in vitro differentiation of human ReNCell neural progenitor cells. Epigenetics 2023; 18:2276425. [PMID: 37976174 PMCID: PMC10769555 DOI: 10.1080/15592294.2023.2276425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
An immortalized neural cell line derived from the human ventral mesencephalon, called ReNCell, and its MeCP2 knock out were used. With it, we characterized the chromatin compositional transitions undergone during differentiation, with special emphasis on linker histones. While the WT cells displayed the development of dendrites and axons the KO cells did not, despite undergoing differentiation as monitored by NeuN. ReNCell expressed minimal amounts of histone H1.0 and their linker histone complement consisted mainly of histone H1.2, H1.4 and H1.5. The overall level of histone H1 exhibited a trend to increase during the differentiation of MeCP2 KO cells. The phosphorylation levels of histone H1 proteins decreased dramatically during ReNCell's cell differentiation independently of the presence of MeCP2. Immunofluorescence analysis showed that MeCP2 exhibits an extensive co-localization with linker histones. Interestingly, the average size of the nucleus decreased during differentiation but in the MeCP2 KO cells, the smaller size of the nuclei at the start of differentiation increased by almost 40% after differentiation by 8 days (8 DIV). In summary, our data provide a compelling perspective on the dynamic changes of H1 histones during neural differentiation, coupled with the intricate interplay between H1 variants and MeCP2.Abbreviations: ACN, acetonitrile; A230, absorbance at 230 nm; bFGF, basic fibroblast growth factor; CM, chicken erythrocyte histone marker; CNS, central nervous system; CRISPR, clustered regulated interspaced short palindromic repeatsDAPI, 4,'6-diaminidino-2-phenylindole; DIV, days in vitro (days after differentiation is induced); DMEM, Dulbecco's modified Eagle medium; EGF, epidermal growth factor; ESC, embryonic stem cell; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFAP, glial fibrillary acidic proteinHPLC, high-performance liquid chromatography; IF, immunofluorescence; iPSCs, induced pluripotent stem cells; MAP2, microtubule-associated protein 2; MBD, methyl-binding domain; MeCP2, methyl-CpG binding protein 2; MS, mass spectrometry; NCP, nucleosome core particle; NeuN, neuron nuclear antigen; NPC, neural progenitor cellPAGE, polyacrylamide gel electrophoresis; PBS, phosphate buffered saline; PFA, paraformaldehyde; PTM, posttranslational modification; RP-HPLC, reversed phase HPLC; ReNCells, ReNCells VM; RPLP0, ribosomal protein lateral stalk subunit P0; RT-qPCR, reverse transcription quantitative polymerase-chain reaction; RTT, Rett Syndrome; SDS, sodium dodecyl sulphate; TAD, topologically associating domain; Triple KO, triple knockout.
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Affiliation(s)
- Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- National Council for Scientific and Technological Development (CNPq), Brasilia, Federal District, Brazil
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Larry Reser
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Robert Chow
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Kerry Delaney
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Mark M. Ross
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- GermansTrias i Pujol Health Science Research Institute, Badalona, Barcelona, Catalonia, Spain
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Li Z, Quan B, Li X, Xiong W, Peng Z, Liu J, Wang Y. A proteomic and phosphoproteomic landscape of spinal cord injury. Neurosci Lett 2023; 814:137449. [PMID: 37597742 DOI: 10.1016/j.neulet.2023.137449] [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: 03/27/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Spinal cord injury (SCI) is a devastating trauma of the central nervous system, with high levels of morbidity, disability, and mortality. To explore the underlying mechanism of SCI, we analyzed the proteome and phosphoproteome of rats at one week after SCI. We identified 465 up-regulated and 129 down-regulated differentially expressed proteins (DEPs), as well as 184 up-regulated and 40 down-regulated differentially expressed phosphoproteins (DEPPs). Using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, we identified the biological characteristics of these proteins from the perspectives of cell component, biological process, and molecular function. We also found a lot of enriched functional pathways such as GABAergic synapse pathway, ErbB signaling pathway, tight junction, adherens junction. The integrated analysis of proteomics and phosphoproteomics yielded 22 differently expressed co-identified proteins of DEPs and DEPPs, which revealed strongly correlative patterns. These findings may help clarify the potential mechanisms of trauma and repair in SCI and may guide the development of novel treatments.
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Affiliation(s)
- Zhigang Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; The Fifth Department of Orthopedics, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Bingxuan Quan
- The Fifth Department of Orthopedics, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Xiuyan Li
- The Fifth Department of Orthopedics, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Wei Xiong
- Department of Orthopedic Surgery, Limin Hospital of Weihai High District, Weihai, China
| | - Zhibin Peng
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingsong Liu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yansong Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; NHC Key Laboratory of Cell Transplantation, Harbin Medical University, Harbin, China; Heilongjiang Provincial Key Laboratory of Hard Tissue Development and Regeneration, Harbin Medical University, Harbin, China.
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The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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5
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Soshnev AA, Allis CD, Cesarman E, Melnick AM. Histone H1 Mutations in Lymphoma: A Link(er) between Chromatin Organization, Developmental Reprogramming, and Cancer. Cancer Res 2021; 81:6061-6070. [PMID: 34580064 PMCID: PMC8678342 DOI: 10.1158/0008-5472.can-21-2619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
Aberrant cell fate decisions due to transcriptional misregulation are central to malignant transformation. Histones are the major constituents of chromatin, and mutations in histone-encoding genes are increasingly recognized as drivers of oncogenic transformation. Mutations in linker histone H1 genes were recently identified as drivers of peripheral lymphoid malignancy. Loss of H1 in germinal center B cells results in widespread chromatin decompaction, redistribution of core histone modifications, and reactivation of stem cell-specific transcriptional programs. This review explores how linker histones and mutations therein regulate chromatin structure, highlighting reciprocal relationships between epigenetic circuits, and discusses the emerging role of aberrant three-dimensional chromatin architecture in malignancy.
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Affiliation(s)
- Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York.
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology & Medical Oncology, Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York.
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6
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Abstract
In this review, Prendergast and Reinberg discuss the likelihood that the family of histone H1 variants may be key to understanding several fundamental processes in chromatin biology and underscore their particular contributions to distinctly significant chromatin-related processes. Major advances in the chromatin and epigenetics fields have uncovered the importance of core histones, histone variants and their post-translational modifications (PTMs) in modulating chromatin structure. However, an acutely understudied related feature of chromatin structure is the role of linker histone H1. Previous assumptions of the functional redundancy of the 11 nonallelic H1 variants are contrasted by their strong evolutionary conservation, variability in their potential PTMs, and increased reports of their disparate functions, sub-nuclear localizations and unique expression patterns in different cell types. The commonly accepted notion that histone H1 functions solely in chromatin compaction and transcription repression is now being challenged by work from multiple groups. These studies highlight histone H1 variants as underappreciated facets of chromatin dynamics that function independently in various chromatin-based processes. In this review, we present notable findings involving the individual somatic H1 variants of which there are seven, underscoring their particular contributions to distinctly significant chromatin-related processes.
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Affiliation(s)
- Laura Prendergast
- Howard Hughes Medical Institute, New York University Langone Health, New York, New York 10016, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical School, New York, New York 10016, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University Langone Health, New York, New York 10016, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical School, New York, New York 10016, USA
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Saha A, Dalal Y. A glitch in the snitch: the role of linker histone H1 in shaping the epigenome in normal and diseased cells. Open Biol 2021; 11:210124. [PMID: 34343462 PMCID: PMC8331230 DOI: 10.1098/rsob.210124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Histone H1s or the linker histones are a family of dynamic chromatin compacting proteins that are essential for higher-order chromatin organization. These highly positively charged proteins were previously thought to function solely as repressors of transcription. However, over the last decade, there is a growing interest in understanding this multi-protein family, finding that not all variants act as repressors. Indeed, the H1 family members appear to have distinct affinities for chromatin and may potentially affect distinct functions. This would suggest a more nuanced contribution of H1 to chromatin organization. The advent of new technologies to probe H1 dynamics in vivo, combined with powerful computational biology, and in vitro imaging tools have greatly enhanced our knowledge of the mechanisms by which H1 interacts with chromatin. This family of proteins can be metaphorically compared to the Golden Snitch from the Harry Potter series, buzzing on and off several regions of the chromatin, in combat with competing transcription factors and chromatin remodellers, thereby critical to the epigenetic endgame on short and long temporal scales in the life of the nucleus. Here, we summarize recent efforts spanning structural, computational, genomic and genetic experiments which examine the linker histone as an unseen architect of chromatin fibre in normal and diseased cells and explore unanswered fundamental questions in the field.
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Affiliation(s)
- Ankita Saha
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yamini Dalal
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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8
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Site-Specific Phosphorylation of Histone H1.4 Is Associated with Transcription Activation. Int J Mol Sci 2020; 21:ijms21228861. [PMID: 33238524 PMCID: PMC7700352 DOI: 10.3390/ijms21228861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 01/05/2023] Open
Abstract
Core histone variants, such as H2A.X and H3.3, serve specialized roles in chromatin processes that depend on the genomic distributions and amino acid sequence differences of the variant proteins. Modifications of these variants alter interactions with other chromatin components and thus the protein’s functions. These inferences add to the growing arsenal of evidence against the older generic view of those linker histones as redundant repressors. Furthermore, certain modifications of specific H1 variants can confer distinct roles. On the one hand, it has been reported that the phosphorylation of H1 results in its release from chromatin and the subsequent transcription of HIV-1 genes. On the other hand, recent evidence indicates that phosphorylated H1 may in fact be associated with active promoters. This conflict suggests that different H1 isoforms and modified versions of these variants are not redundant when together but may play distinct functional roles. Here, we provide the first genome-wide evidence that when phosphorylated, the H1.4 variant remains associated with active promoters and may even play a role in transcription activation. Using novel, highly specific antibodies, we generated the first genome-wide view of the H1.4 isoform phosphorylated at serine 187 (pS187-H1.4) in estradiol-inducible MCF7 cells. We observe that pS187-H1.4 is enriched primarily at the transcription start sites (TSSs) of genes activated by estradiol treatment and depleted from those that are repressed. We also show that pS187-H1.4 associates with ‘early estrogen response’ genes and stably interacts with RNAPII. Based on the observations presented here, we propose that phosphorylation at S187 by CDK9 represents an early event required for gene activation. This event may also be involved in the release of promoter-proximal polymerases to begin elongation by interacting directly with the polymerase or other parts of the transcription machinery. Although we focused on estrogen-responsive genes, taking into account previous evidence of H1.4′s enrichment of promoters of pluripotency genes, and its involvement with rDNA activation, we propose that H1.4 phosphorylation for gene activation may be a more global observation.
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Senigagliesi B, Penzo C, Severino LU, Maraspini R, Petrosino S, Morales-Navarrete H, Pobega E, Ambrosetti E, Parisse P, Pegoraro S, Manfioletti G, Casalis L, Sgarra R. The High Mobility Group A1 (HMGA1) Chromatin Architectural Factor Modulates Nuclear Stiffness in Breast Cancer Cells. Int J Mol Sci 2019; 20:2733. [PMID: 31167352 PMCID: PMC6600462 DOI: 10.3390/ijms20112733] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022] Open
Abstract
Plasticity is an essential condition for cancer cells to invade surrounding tissues. The nucleus is the most rigid cellular organelle and it undergoes substantial deformations to get through environmental constrictions. Nuclear stiffness mostly depends on the nuclear lamina and chromatin, which in turn might be affected by nuclear architectural proteins. Among these is the HMGA1 (High Mobility Group A1) protein, a factor that plays a causal role in neoplastic transformation and that is able to disentangle heterochromatic domains by H1 displacement. Here we made use of atomic force microscopy to analyze the stiffness of breast cancer cellular models in which we modulated HMGA1 expression to investigate its role in regulating nuclear plasticity. Since histone H1 is the main modulator of chromatin structure and HMGA1 is a well-established histone H1 competitor, we correlated HMGA1 expression and cellular stiffness with histone H1 expression level, post-translational modifications, and nuclear distribution. Our results showed that HMGA1 expression level correlates with nuclear stiffness, is associated to histone H1 phosphorylation status, and alters both histone H1 chromatin distribution and expression. These data suggest that HMGA1 might promote chromatin relaxation through a histone H1-mediated mechanism strongly impacting on the invasiveness of cancer cells.
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Affiliation(s)
| | - Carlotta Penzo
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Luisa Ulloa Severino
- Nano Innovation Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy.
| | - Riccardo Maraspini
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Sara Petrosino
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy.
| | | | - Enrico Pobega
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Elena Ambrosetti
- Nano Innovation Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy.
| | - Pietro Parisse
- Nano Innovation Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy.
| | - Silvia Pegoraro
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy.
| | | | - Loredana Casalis
- Nano Innovation Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy.
| | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy.
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Topalovic V, Krstic A, Schwirtlich M, Dolfini D, Mantovani R, Stevanovic M, Mojsin M. Epigenetic regulation of human SOX3 gene expression during early phases of neural differentiation of NT2/D1 cells. PLoS One 2017; 12:e0184099. [PMID: 28886103 PMCID: PMC5590877 DOI: 10.1371/journal.pone.0184099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/17/2017] [Indexed: 01/09/2023] Open
Abstract
Sox3/SOX3 is one of the earliest neural markers in vertebrates. Together with the Sox1/SOX1 and Sox2/SOX2 genes it is implicated in the regulation of stem cell identity. In the present study, we performed the first analysis of epigenetic mechanisms (DNA methylation and histone marks) involved in the regulation of the human SOX3 gene expression during RA-induced neural differentiation of NT2/D1 cells. We show that the promoter of the human SOX3 gene is extremely hypomethylated both in undifferentiated NT2/D1 cells and during the early phases of RA-induced neural differentiation. By employing chromatin immunoprecipitation, we analyze several histone modifications across different regions of the SOX3 gene and their dynamics following initiation of differentiation. In the same timeframe we investigate profiles of selected histone marks on the promoters of human SOX1 and SOX2 genes. We demonstrate differences in histone signatures of SOX1, SOX2 and SOX3 genes. Considering the importance of SOXB1 genes in the process of neural differentiation, the present study contributes to a better understanding of epigenetic mechanisms implicated in the regulation of pluripotency maintenance and commitment towards the neural lineage.
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Affiliation(s)
- Vladanka Topalovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Marija Schwirtlich
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Marija Mojsin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- * E-mail:
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