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Nishitani A, Hiramatsu K, Kadooka C, Mori K, Okutsu K, Yoshizaki Y, Takamine K, Tashiro K, Goto M, Tamaki H, Futagami T. Expression of heterochromatin protein 1 affects citric acid production in Aspergillus luchuensis mut. kawachii. J Biosci Bioeng 2023; 136:443-451. [PMID: 37775438 DOI: 10.1016/j.jbiosc.2023.09.004] [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: 06/11/2023] [Revised: 08/17/2023] [Accepted: 09/07/2023] [Indexed: 10/01/2023]
Abstract
A putative methyltransferase, LaeA, controls citric acid production through epigenetic regulation of the citrate exporter gene, cexA, in the white koji fungus Aspergillus luchuensis mut. kawachii. In this study, we investigated the role of another epigenetic regulator, heterochromatin protein 1, HepA, in citric acid production. The ΔhepA strain exhibited reduced citric acid production in liquid culture, although to a lesser extent compared to the ΔlaeA strain. In addition, the ΔlaeA ΔhepA strain showed citric acid production similar to the ΔlaeA strain, indicating that HepA plays a role in citric acid production, albeit with a less-significant regulatory effect than LaeA. RNA-seq analysis revealed that the transcriptomic profiles of the ΔhepA and ΔlaeA strains were similar, and the expression level of cexA was reduced in both strains. These findings suggest that the genes regulated by HepA are similar to those regulated by LaeA in A. luchuensis mut. kawachii. However, the reductions in citric acid production and cexA expression observed in the disruptants were mitigated in rice koji, a solid-state culture. Thus, the mechanism by which citric acid production is regulated differs between liquid and solid cultivation. Further investigation is thus needed to understand the regulatory mechanism in koji.
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Affiliation(s)
- Atsushi Nishitani
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Center for Advanced Science Research and Promotion, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kentaro Hiramatsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
| | - Chihiro Kadooka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto 860-0082, Japan
| | - Kazuki Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Kayu Okutsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Yumiko Yoshizaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kazunori Takamine
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Masatoshi Goto
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Hisanori Tamaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
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Stylianakis E, Chan JPK, Law PP, Jiang Y, Khadayate S, Karimi MM, Festenstein R, Vannier JB. Mouse HP1γ regulates TRF1 expression and telomere stability. Life Sci 2023; 331:122030. [PMID: 37598977 DOI: 10.1016/j.lfs.2023.122030] [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: 11/29/2022] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
AIMS Telomeric repeat-containing RNAs are long non-coding RNAs generated from the telomeres. TERRAs are essential for the establishment of heterochromatin marks at telomeres, which serve for the binding of members of the heterochromatin protein 1 (HP1) protein family of epigenetic modifiers involved with chromatin compaction and gene silencing. While HP1γ is enriched on gene bodies of actively transcribed human and mouse genes, it is unclear if its transcriptional role is important for HP1γ function in telomere cohesion and telomere maintenance. We aimed to study the effect of mouse HP1γ on the transcription of telomere factors and molecules that can affect telomere maintenance. MAIN METHODS We investigated the telomere function of HP1γ by using HP1γ deficient mouse embryonic fibroblasts (MEFs). We used gene expression analysis of HP1γ deficient MEFs and validated the molecular and mechanistic consequences of HP1γ loss by telomere FISH, immunofluorescence, RT-qPCR and DNA-RNA immunoprecipitation (DRIP). KEY FINDINGS Loss of HP1γ in primary MEFs led to a downregulation of various telomere and telomere-accessory transcripts, including the shelterin protein TRF1. Its downregulation is associated with increased telomere replication stress and DNA damage (γH2AX), effects more profound in females. We suggest that the source for the impaired telomere maintenance is a consequence of increased telomeric DNA-RNA hybrids and TERRAs arising at and from mouse chromosomes 18 and X. SIGNIFICANCE Our results suggest an important transcriptional control by mouse HP1γ of various telomere factors including TRF1 protein and TERRAs that has profound consequences on telomere stability, with a potential sexually dimorphic nature.
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Affiliation(s)
- Emmanouil Stylianakis
- Telomere Replication & Stability group, Medical Research Council London Institute of Medical Sciences, London, United Kingdom; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Jackson Ping Kei Chan
- Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Pui Pik Law
- Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Yi Jiang
- Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Sanjay Khadayate
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mohammad Mahdi Karimi
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Richard Festenstein
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Jean-Baptiste Vannier
- Telomere Replication & Stability group, Medical Research Council London Institute of Medical Sciences, London, United Kingdom; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.
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Noureddine LM, Ablain J, Surmieliova-Garnès A, Jacquemetton J, Pham TH, Marangoni E, Schnitzler A, Bieche I, Badran B, Trédan O, Hussein N, Le Romancer M, Poulard C. PRMT5 triggers glucocorticoid-induced cell migration in triple-negative breast cancer. Life Sci Alliance 2023; 6:e202302009. [PMID: 37536978 PMCID: PMC10400884 DOI: 10.26508/lsa.202302009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
Triple-negative breast cancers (TNBCs) are the most aggressive breast cancers, and therapeutic options mainly rely on chemotherapy and immunotherapy. Although synthetic glucocorticoids (GCs) are given to alleviate the side effects of these treatments, GCs and their receptor, the glucocorticoid receptor (GR), were recently associated with detrimental effects, albeit the mechanisms involved remain elusive. Here, we identified the arginine methyltransferase PRMT5 as a master coregulator of GR, serving as a scaffold protein to recruit phospho-HP1γ and subsequently RNA polymerase II, independently of its methyltransferase activity. Moreover, the GR/PRMT5/HP1γ complex regulated the transcription of GC-target genes involved in cell motility and triggering cell migration of human TNBC cells in vitro and in a zebrafish model. Of note, we observed that GR/PRMT5 interaction was low in primary tumors but significantly increased in residual tumors treated with chemotherapy and GCs in neoadjuvant setting. These data suggest that the routine premedication prescription of GCs for early TNBC patients should be further assessed and that this complex could potentially be modulated to specifically target deleterious GR effects.
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Affiliation(s)
- Lara Malik Noureddine
- Université de Lyon, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Lebanese University, Faculty of Sciences I, Department of Chemistry and Biochemistry, Laboratory of Cancer Biology and Molecular Immunology, Beirut, Lebanon
| | - Julien Ablain
- Université de Lyon, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Ausra Surmieliova-Garnès
- Université de Lyon, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Julien Jacquemetton
- Université de Lyon, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Thuy Ha Pham
- Université de Lyon, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Elisabetta Marangoni
- Institut Curie, Translational Research Department, PSL University, Paris, France
| | | | - Ivan Bieche
- Institut Curie, Department of Genetics, Paris, France
| | - Bassam Badran
- Lebanese University, Faculty of Sciences I, Department of Chemistry and Biochemistry, Laboratory of Cancer Biology and Molecular Immunology, Beirut, Lebanon
| | - Olivier Trédan
- Université de Lyon, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Centre Leon Bérard, Oncology Department, Lyon, France
| | - Nader Hussein
- Lebanese University, Faculty of Sciences I, Department of Chemistry and Biochemistry, Laboratory of Cancer Biology and Molecular Immunology, Beirut, Lebanon
| | - Muriel Le Romancer
- Université de Lyon, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Coralie Poulard
- Université de Lyon, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
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Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast. Biomolecules 2023; 13:biom13020377. [PMID: 36830746 PMCID: PMC9953268 DOI: 10.3390/biom13020377] [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: 01/23/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
DNA is stored in the nucleus of a cell in a folded state; however, only the necessary genetic information is extracted from the required group of genes. The key to extracting genetic information is chromatin ambivalence. Depending on the chromosomal region, chromatin is characterized into low-density "euchromatin" and high-density "heterochromatin", with various factors being involved in its regulation. Here, we focus on chromatin regulation and gene expression by the yeast FACT complex, which functions in both euchromatin and heterochromatin. FACT is known as a histone H2A/H2B chaperone and was initially reported as an elongation factor associated with RNA polymerase II. In budding yeast, FACT activates promoter chromatin by interacting with the transcriptional activators SBF/MBF via the regulation of G1/S cell cycle genes. In fission yeast, FACT plays an important role in the formation of higher-order chromatin structures and transcriptional repression by binding to Swi6, an HP1 family protein, at heterochromatin. This FACT property, which refers to the alternate chromatin-regulation depending on the binding partner, is an interesting phenomenon. Further analysis of nucleosome regulation within heterochromatin is expected in future studies.
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Wistner SC, MacDonald IA, Stanley KA, Hathaway NA. Characterization of Hepatoma-Derived Growth Factor-Related Protein 2 Interactions with Heterochromatin. Cells 2023; 12:325. [PMID: 36672260 PMCID: PMC9856275 DOI: 10.3390/cells12020325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
The expression of genetic information is tightly controlled by chromatin regulatory proteins, including those in the heterochromatin gene repression family. Many of these regulatory proteins work together on the chromatin substrate to precisely regulate gene expression during mammalian development, giving rise to many different tissues in higher organisms from a fixed genomic template. Here we identify and characterize the interactions of two related heterochromatin regulatory proteins, heterochromatin protein 1 alpha (HP1α) and M-phase phosphoprotein 8 (MPP8), with hepatoma-derived growth factor-related protein 2 (HRP2). We find in biochemical experiments that HRP2 copurifies and co-sediments with heterochromatin-associated proteins, including HP1α and MPP8. Using the Chromatin in vivo Assay in multiple cell types, we demonstrate that HP1α-mediated gene repression dynamics are altered by the presence of HRP2. Furthermore, the knockout of HRP2 in MDA-MB-231 cells results in significant changes to chromatin structure and stability, which alter gene expression patterns. Here, we detail a mechanism by which HRP2 contributes to epigenetic transcriptional regulation through engagement with heterochromatin-associated proteins to stabilize the chromatin landscape and influence gene expression.
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Affiliation(s)
- Sarah C. Wistner
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian A. MacDonald
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karly A. Stanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Bunch H. Studying RNA Polymerase II Promoter-Proximal Pausing by In Vitro Immobilized Template and Transcription Assays. Methods Mol Biol 2023; 2693:13-24. [PMID: 37540423 DOI: 10.1007/978-1-0716-3342-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The immobilized template assay is a versatile biochemical method for studying protein-nucleic acid interactions. Using this method, immobilized nucleic acid-associated or specific proteins can be identified and quantified by techniques such as mass spectrometry and immunoblotting. Here, a modified immobilized template assay combined with in vitro transcription assay to study the function of transcription factors and transcriptional activities at the human heat shock protein 70 (HSP70) gene is described. Notably, this method can be applied to study other important genes and transcription factors in vitro.
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Affiliation(s)
- Heeyoun Bunch
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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Herman N, Kadener S, Shifman S. The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes. EMBO Rep 2022; 23:e54720. [PMID: 36245419 PMCID: PMC9724677 DOI: 10.15252/embr.202254720] [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: 01/24/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Insulator proteins located at the boundaries of topological associated domains (TAD) are involved in higher-order chromatin organization and transcription regulation. However, it is still not clear how long-range contacts contribute to transcriptional regulation. Here, we show that relative-of-WOC (ROW) is essential for the long-range transcription regulation mediated by the boundary element-associated factor of 32kD (BEAF-32). We find that ROW physically interacts with heterochromatin proteins (HP1b and HP1c) and the insulator protein (BEAF-32). These proteins interact at TAD boundaries where ROW, through its AT-hook motifs, binds AT-rich sequences flanked by BEAF-32-binding sites and motifs. Knockdown of row downregulates genes that are long-range targets of BEAF-32 and bound indirectly by ROW (without binding motif). Analyses of high-throughput chromosome conformation capture (Hi-C) data reveal long-range interactions between promoters of housekeeping genes bound directly by ROW and promoters of developmental genes bound indirectly by ROW. Thus, our results show cooperation between BEAF-32 and the ROW complex, including HP1 proteins, to regulate the transcription of developmental and inducible genes through long-range interactions.
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Affiliation(s)
- Neta Herman
- Department of Genetics, The Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | | | - Sagiv Shifman
- Department of Genetics, The Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
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Deficiency of the Two-Pore Potassium Channel KCNK9 Impairs Intestinal Epithelial Cell Survival and Aggravates Dextran Sodium Sulfate-Induced Colitis. Cell Mol Gastroenterol Hepatol 2022; 14:1199-1211. [PMID: 35973573 PMCID: PMC9579309 DOI: 10.1016/j.jcmgh.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS The 2-pore potassium channel subfamily K member 9 (KCNK9) regulates intracellular calcium concentration and thus modulates cell survival and inflammatory signaling pathways. It also was recognized as a risk allele for inflammatory bowel disease. However, it remains unclear whether KCNK9 modulates inflammatory bowel disease via its impact on immune cell function or whether its influence on calcium homeostasis also is relevant in intestinal epithelial cells. METHODS Kcnk9-/- mice were challenged with 3% dextran sulfate sodium (DSS) to induce experimental acute colitis. Primary cultures of intestinal epithelial cells were generated, and expression of potassium channels as well as cytosolic calcium levels and susceptibility to apoptosis were evaluated. Furthermore, we evaluated whether KCNK9 deficiency was compensated by the closely related 2-pore potassium channel KCNK3 in vivo or in vitro. RESULTS Compared with controls, KCNK9 deficiency or its pharmacologic blockade were associated with aggravated DSS-induced colitis compared with wild-type animals. In the absence of KCNK9, intestinal epithelial cells showed increased intracellular calcium levels and were more prone to mitochondrial damage and caspase-9-dependent apoptosis. We found that expression of KCNK3 was increased in Kcnk9-/- mice but did not prevent apoptosis after DSS exposure. Conversely, increased levels of KCNK9 in Kcnk3-/- mice were associated with an ameliorated course of DSS-induced colitis. CONCLUSIONS KCNK9 enhances mitochondrial stability, reduces apoptosis, und thus supports epithelial cell survival after DSS exposure in vivo and in vitro. Conversely, its increased expression in Kcnk3-/- resulted in less mitochondrial damage and apoptosis and was associated with beneficial outcomes in DSS-induced colitis.
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Schoelz JM, Riddle NC. Functions of HP1 proteins in transcriptional regulation. Epigenetics Chromatin 2022; 15:14. [PMID: 35526078 PMCID: PMC9078007 DOI: 10.1186/s13072-022-00453-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023] Open
Abstract
In eukaryotes, DNA is packaged into chromatin, which presents significant barriers to transcription. Non-histone chromatin proteins such as the Heterochromatin Protein 1 (HP1) proteins are critical regulators of transcription, contributing to gene regulation through a variety of molecular mechanisms. HP1 proteins are highly conserved, and many eukaryotic genomes contain multiple HP1 genes. Given the presence of multiple HP1 family members within a genome, HP1 proteins can have unique as well as shared functions. Here, we review the mechanisms by which HP1 proteins contribute to the regulation of transcription. Focusing on the Drosophila melanogaster HP1 proteins, we examine the role of these proteins in regulating the transcription of genes, transposable elements, and piRNA clusters. In D. melanogaster, as in other species, HP1 proteins can act as transcriptional repressors and activators. The available data reveal that the precise impact of HP1 proteins on gene expression is highly context dependent, on the specific HP1 protein involved, on its protein partners present, and on the specific chromatin context the interaction occurs in. As a group, HP1 proteins utilize a variety of mechanisms to contribute to transcriptional regulation, including both transcriptional (i.e. chromatin-based) and post-transcriptional (i.e. RNA-based) processes. Despite extensive studies of this important protein family, open questions regarding their functions in gene regulation remain, specifically regarding the role of hetero- versus homodimerization and post-translational modifications of HP1 proteins.
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Affiliation(s)
- John M Schoelz
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole C Riddle
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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10
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Jeronimo C, Robert F. The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 2022; 13:16-38. [PMID: 35485711 PMCID: PMC9467567 DOI: 10.1080/21541264.2022.2069995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
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11
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Walle T, Kraske JA, Liao B, Lenoir B, Timke C, von Bohlen und Halbach E, Tran F, Griebel P, Albrecht D, Ahmed A, Suarez-Carmona M, Jiménez-Sánchez A, Beikert T, Tietz-Dahlfuß A, Menevse AN, Schmidt G, Brom M, Pahl JHW, Antonopoulos W, Miller M, Perez RL, Bestvater F, Giese NA, Beckhove P, Rosenstiel P, Jäger D, Strobel O, Pe’er D, Halama N, Debus J, Cerwenka A, Huber PE. Radiotherapy orchestrates natural killer cell dependent antitumor immune responses through CXCL8. SCIENCE ADVANCES 2022; 8:eabh4050. [PMID: 35319989 PMCID: PMC8942354 DOI: 10.1126/sciadv.abh4050] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 01/31/2022] [Indexed: 05/17/2023]
Abstract
Radiotherapy is a mainstay cancer therapy whose antitumor effects partially depend on T cell responses. However, the role of Natural Killer (NK) cells in radiotherapy remains unclear. Here, using a reverse translational approach, we show a central role of NK cells in the radiation-induced immune response involving a CXCL8/IL-8-dependent mechanism. In a randomized controlled pancreatic cancer trial, CXCL8 increased under radiotherapy, and NK cell positively correlated with prolonged overall survival. Accordingly, NK cells preferentially infiltrated irradiated pancreatic tumors and exhibited CD56dim-like cytotoxic transcriptomic states. In experimental models, NF-κB and mTOR orchestrated radiation-induced CXCL8 secretion from tumor cells with senescence features causing directional migration of CD56dim NK cells, thus linking senescence-associated CXCL8 release to innate immune surveillance of human tumors. Moreover, combined high-dose radiotherapy and adoptive NK cell transfer improved tumor control over monotherapies in xenografted mice, suggesting NK cells combined with radiotherapy as a rational cancer treatment strategy.
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Affiliation(s)
- Thomas Walle
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Medical Oncology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Immunobiochemistry and MI3, Mannheim Institute for Innate Immunoscience, Heidelberg University, Medical Faculty Mannheim, Mannheim, Germany
- Corresponding author. (T.W.); (P.E.H.)
| | - Joscha A. Kraske
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiooncology and Radiotherapy, University Hospital Heidelberg, Heidelberg, Germany
| | - Boyu Liao
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiooncology and Radiotherapy, University Hospital Heidelberg, Heidelberg, Germany
| | - Bénédicte Lenoir
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carmen Timke
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, St. Franziskus Hospital, Flensburg, Germany
| | - Emilia von Bohlen und Halbach
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Medical Oncology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Paul Griebel
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Dorothee Albrecht
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Azaz Ahmed
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Meggy Suarez-Carmona
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alejandro Jiménez-Sánchez
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tizian Beikert
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiooncology and Radiotherapy, University Hospital Heidelberg, Heidelberg, Germany
| | - Alexandra Tietz-Dahlfuß
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ayse Nur Menevse
- Leibniz Institute for Immunotherapy, Division of Interventional Immunology, Regensburg, Germany
| | - Gabriele Schmidt
- Core Facility Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Brom
- Core Facility Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens H. W. Pahl
- Department of Immunobiochemistry and MI3, Mannheim Institute for Innate Immunoscience, Heidelberg University, Medical Faculty Mannheim, Mannheim, Germany
| | | | - Matthias Miller
- Department of Immunobiochemistry and MI3, Mannheim Institute for Innate Immunoscience, Heidelberg University, Medical Faculty Mannheim, Mannheim, Germany
| | - Ramon Lopez Perez
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiooncology and Radiotherapy, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Bestvater
- Core Facility Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nathalia A. Giese
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Philipp Beckhove
- Leibniz Institute for Immunotherapy, Division of Interventional Immunology, Regensburg, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Medical Oncology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Dana Pe’er
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Medical Oncology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz Center for Translational Oncology (HITRON), Mainz, Germany
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen Debus
- Department of Radiooncology and Radiotherapy, University Hospital Heidelberg, Heidelberg, Germany
- Heidelberg Ion Therapy Center (HIT), Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany
| | - Adelheid Cerwenka
- Department of Immunobiochemistry and MI3, Mannheim Institute for Innate Immunoscience, Heidelberg University, Medical Faculty Mannheim, Mannheim, Germany
| | - Peter E. Huber
- Department of Molecular and Radiooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiooncology and Radiotherapy, University Hospital Heidelberg, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany
- Corresponding author. (T.W.); (P.E.H.)
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12
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Schoelz JM, Feng JX, Riddle NC. The Drosophila HP1 family is associated with active gene expression across chromatin contexts. Genetics 2021; 219:6321239. [PMID: 34849911 DOI: 10.1093/genetics/iyab108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/07/2021] [Indexed: 11/13/2022] Open
Abstract
Drosophila Heterochromatin Protein 1a (HP1a) is essential for heterochromatin formation and is involved in transcriptional silencing. However, certain loci require HP1a to be transcribed. One model posits that HP1a acts as a transcriptional silencer within euchromatin while acting as an activator within heterochromatin. However, HP1a has been observed as an activator of a set of euchromatic genes. Therefore, it is not clear whether, or how, chromatin context informs the function of HP1 proteins. To understand the role of HP1 proteins in transcription, we examined the genome-wide binding profile of HP1a as well as two other Drosophila HP1 family members, HP1B and HP1C, to determine whether coordinated binding of these proteins is associated with specific transcriptional outcomes. We found that HP1 proteins share many of their endogenous binding targets. These genes are marked by active histone modifications and are expressed at higher levels than nontarget genes in both heterochromatin and euchromatin. In addition, HP1 binding targets displayed increased RNA polymerase pausing compared with nontarget genes. Specifically, colocalization of HP1B and HP1C was associated with the highest levels of polymerase pausing and gene expression. Analysis of HP1 null mutants suggests these proteins coordinate activity at transcription start sites to regulate transcription. Depletion of HP1B or HP1C alters expression of protein-coding genes bound by HP1 family members. Our data broaden understanding of the mechanism of transcriptional activation by HP1a and highlight the need to consider particular protein-protein interactions, rather than broader chromatin context, to predict impacts of HP1 at transcription start sites.
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Affiliation(s)
- John M Schoelz
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Justina X Feng
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
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13
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Uruci S, Lo CSY, Wheeler D, Taneja N. R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde. Int J Mol Sci 2021; 22:ijms22168850. [PMID: 34445553 PMCID: PMC8396322 DOI: 10.3390/ijms22168850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
Since their discovery, R-loops have been associated with both physiological and pathological functions that are conserved across species. R-loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R-loop accumulation as well as to resolve them. A growing body of evidence correlates R-loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R-loops homeostasis remains unclear. This review covers various mechanisms precluding R-loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R-loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication-transcription conflicts. Finally, we discuss the potential role of several Chro-Mates (chromatin modifiers and remodelers) in the likely differentiation between persistent/detrimental R-loops and transient/benign R-loops that assist in various physiological processes relevant for therapeutic interventions.
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Affiliation(s)
- Sidrit Uruci
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - Calvin Shun Yu Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA;
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
- Correspondence:
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14
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Takahata S, Chida S, Ohnuma A, Ando M, Asanuma T, Murakami Y. Two secured FACT recruitment mechanisms are essential for heterochromatin maintenance. Cell Rep 2021; 36:109540. [PMID: 34407404 DOI: 10.1016/j.celrep.2021.109540] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/01/2021] [Accepted: 07/26/2021] [Indexed: 11/18/2022] Open
Abstract
FACT (facilitate chromatin transcription) is involved in heterochromatic silencing, but its mechanisms and function remain unclear. We reveal that the Spt16 recruitment mechanism operates in two distinct ways in heterochromatin. First, Pob3 mediates Spt16 recruitment onto the heterochromatin through its Spt16 dimerization and tandem PH domains. Without Pob3, Spt16 recruitment is partially reduced, exhibiting a silencing defect and impaired H2A/H2B organization. Second, heterochromatin protein 1 (HP1)/Swi6 mediates Spt16 recruitment onto the heterochromatin by physical interaction of the Swi6 chromo-shadow domain (CSD) and Spt16 peptidase-like domains. Several CSD mutants are tested for Spt16 binding activity, and the charged loop connecting β1 and β2 is critical for Spt16 binding and heterochromatic silencing. Loss of these pathways causes a severe defect in H3K9 methylation and HP1/Swi6 localization in the pericentromeric region, exhibiting transcriptional silencing defects and disordered heterochromatin. Our findings suggest that FACT and HP1/Swi6 work intimately to regulate heterochromatin organization.
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Affiliation(s)
- Shinya Takahata
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.
| | - Saori Chida
- Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Aoi Ohnuma
- Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Motoyoshi Ando
- Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takahiro Asanuma
- Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yota Murakami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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15
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Jeronimo C, Angel A, Nguyen VQ, Kim JM, Poitras C, Lambert E, Collin P, Mellor J, Wu C, Robert F. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner. Mol Cell 2021; 81:3542-3559.e11. [PMID: 34380014 DOI: 10.1016/j.molcel.2021.07.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 05/25/2021] [Accepted: 07/12/2021] [Indexed: 12/29/2022]
Abstract
The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Vu Q Nguyen
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jee Min Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Christian Poitras
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Elie Lambert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Pierre Collin
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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16
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Vorobyeva NE, Mazina MY. The Elongation Regulators and Architectural Proteins as New Participants of Eukaryotic Gene Transcription. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421060144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Casale AM, Cappucci U, Piacentini L. Unravelling HP1 functions: post-transcriptional regulation of stem cell fate. Chromosoma 2021; 130:103-111. [PMID: 34128099 PMCID: PMC8426308 DOI: 10.1007/s00412-021-00760-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Heterochromatin protein 1 (HP1) is a non-histone chromosomal protein first identified in Drosophila as a major component of constitutive heterochromatin, required for stable epigenetic gene silencing in many species including humans. Over the years, several studies have highlighted additional roles of HP1 in different cellular processes including telomere maintenance, DNA replication and repair, chromosome segregation and, surprisingly, positive regulation of gene expression. In this review, we briefly summarize past research and recent results supporting the unexpected and emerging role of HP1 in activating gene expression. In particular, we discuss the role of HP1 in post-transcriptional regulation of mRNA processing because it has proved decisive in the control of germline stem cells homeostasis in Drosophila and has certainly added a new dimension to our understanding on HP1 targeting and functions in epigenetic regulation of stem cell behaviour.
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Affiliation(s)
- Assunta Maria Casale
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.
| | - Ugo Cappucci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Lucia Piacentini
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.
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18
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Sun J, Wang X, Xu RG, Mao D, Shen D, Wang X, Qiu Y, Han Y, Lu X, Li Y, Che Q, Zheng L, Peng P, Kang X, Zhu R, Jia Y, Wang Y, Liu LP, Chang Z, Ji JY, Wang Z, Liu Q, Li S, Sun FL, Ni JQ. HP1c regulates development and gut homeostasis by suppressing Notch signaling through Su(H). EMBO Rep 2021; 22:e51298. [PMID: 33594776 DOI: 10.15252/embr.202051298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/01/2021] [Accepted: 01/13/2021] [Indexed: 12/30/2022] Open
Abstract
Notch signaling and epigenetic factors are known to play critical roles in regulating tissue homeostasis in most multicellular organisms, but how Notch signaling coordinates with epigenetic modulators to control differentiation remains poorly understood. Here, we identify heterochromatin protein 1c (HP1c) as an essential epigenetic regulator of gut homeostasis in Drosophila. Specifically, we observe that HP1c loss-of-function phenotypes resemble those observed after Notch signaling perturbation and that HP1c interacts genetically with components of the Notch pathway. HP1c represses the transcription of Notch target genes by directly interacting with Suppressor of Hairless (Su(H)), the key transcription factor of Notch signaling. Moreover, phenotypes caused by depletion of HP1c in Drosophila can be rescued by expressing human HP1γ, suggesting that HP1γ functions similar to HP1c in Drosophila. Taken together, our findings reveal an essential role of HP1c in normal development and gut homeostasis by suppressing Notch signaling.
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Affiliation(s)
- Jin Sun
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xia Wang
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Rong-Gang Xu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Decai Mao
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Sichuan Academy of Grassland Science, Chengdu, China
| | - Da Shen
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Xin Wang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics/Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Yuhao Qiu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Yuting Han
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Xinyi Lu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Yutong Li
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Qinyun Che
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Li Zheng
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Ping Peng
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Xuan Kang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai, China
| | - Ruibao Zhu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Yu Jia
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Yinyin Wang
- State Key Laboratory of Membrane Biology, School of Medicine and the School of Life Sciences, Tsinghua University, Beijing, China
| | - Lu-Ping Liu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Zhijie Chang
- State Key Laboratory of Membrane Biology, School of Medicine and the School of Life Sciences, Tsinghua University, Beijing, China
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX, USA
| | - Zhao Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qingfei Liu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Shao Li
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics/Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Fang-Lin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai, China
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsingdao Advanced Research Institute, Tongji University, Qingdao, China
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19
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Zaidan NZ, Sridharan R. HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells. Nucleic Acids Res 2020; 48:12660-12674. [PMID: 33237287 PMCID: PMC7736818 DOI: 10.1093/nar/gkaa1091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/12/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency.
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Affiliation(s)
- Nur Zafirah Zaidan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA
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20
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Geng Z, Gao Z. Mammalian PRC1 Complexes: Compositional Complexity and Diverse Molecular Mechanisms. Int J Mol Sci 2020; 21:E8594. [PMID: 33202645 PMCID: PMC7697839 DOI: 10.3390/ijms21228594] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Polycomb group (PcG) proteins function as vital epigenetic regulators in various biological processes, including pluripotency, development, and carcinogenesis. PcG proteins form multicomponent complexes, and two major types of protein complexes have been identified in mammals to date, Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The PRC1 complexes are composed in a hierarchical manner in which the catalytic core, RING1A/B, exclusively interacts with one of six Polycomb group RING finger (PCGF) proteins. This association with specific PCGF proteins allows for PRC1 to be subdivided into six distinct groups, each with their own unique modes of action arising from the distinct set of associated proteins. Historically, PRC1 was considered to be a transcription repressor that deposited monoubiquitylation of histone H2A at lysine 119 (H2AK119ub1) and compacted local chromatin. More recently, there is increasing evidence that demonstrates the transcription activation role of PRC1. Moreover, studies on the higher-order chromatin structure have revealed a new function for PRC1 in mediating long-range interactions. This provides a different perspective regarding both the transcription activation and repression characteristics of PRC1. This review summarizes new advancements regarding the composition of mammalian PRC1 and accompanying explanations of how diverse PRC1-associated proteins participate in distinct transcription regulation mechanisms.
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Affiliation(s)
- Zhuangzhuang Geng
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Zhonghua Gao
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
- Penn State Hershey Cancer Institute, Hershey, PA 17033, USA
- The Stem Cell and Regenerative Biology Program, Penn State College of Medicine, Hershey, PA 17033, USA
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21
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Meyer-Nava S, Nieto-Caballero VE, Zurita M, Valadez-Graham V. Insights into HP1a-Chromatin Interactions. Cells 2020; 9:E1866. [PMID: 32784937 PMCID: PMC7465937 DOI: 10.3390/cells9081866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
Understanding the packaging of DNA into chromatin has become a crucial aspect in the study of gene regulatory mechanisms. Heterochromatin establishment and maintenance dynamics have emerged as some of the main features involved in genome stability, cellular development, and diseases. The most extensively studied heterochromatin protein is HP1a. This protein has two main domains, namely the chromoshadow and the chromodomain, separated by a hinge region. Over the years, several works have taken on the task of identifying HP1a partners using different strategies. In this review, we focus on describing these interactions and the possible complexes and subcomplexes associated with this critical protein. Characterization of these complexes will help us to clearly understand the implications of the interactions of HP1a in heterochromatin maintenance, heterochromatin dynamics, and heterochromatin's direct relationship to gene regulation and chromatin organization.
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Affiliation(s)
| | | | | | - Viviana Valadez-Graham
- Instituto de Biotecnología, Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62210, Mexico; (S.M.-N.); (V.E.N.-C.); (M.Z.)
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22
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Shukla A, Ramirez NGP, D’Orso I. HIV-1 Proviral Transcription and Latency in the New Era. Viruses 2020; 12:v12050555. [PMID: 32443452 PMCID: PMC7291205 DOI: 10.3390/v12050555] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
Three decades of extensive work in the HIV field have revealed key viral and host cell factors controlling proviral transcription. Various models of transcriptional regulation have emerged based on the collective information from in vitro assays and work in both immortalized and primary cell-based models. Here, we provide a recount of the past and current literature, highlight key regulatory aspects, and further describe potential limitations of previous studies. We particularly delve into critical steps of HIV gene expression including the role of the integration site, nucleosome positioning and epigenomics, and the transition from initiation to pausing and pause release. We also discuss open questions in the field concerning the generality of previous regulatory models to the control of HIV transcription in patients under suppressive therapy, including the role of the heterogeneous integration landscape, clonal expansion, and bottlenecks to eradicate viral persistence. Finally, we propose that building upon previous discoveries and improved or yet-to-be discovered technologies will unravel molecular mechanisms of latency establishment and reactivation in a “new era”.
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23
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Di Mauro G, Carbonell A, Escudero-Ferruz P, Azorín F. The zinc-finger proteins WOC and ROW play distinct functions within the HP1c transcription complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194492. [PMID: 32006714 DOI: 10.1016/j.bbagrm.2020.194492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 11/20/2022]
Abstract
In Drosophila, the Heterochromatin Protein 1c (HP1c) forms a transcriptional complex with the zinc-finger proteins WOC and ROW, and the extraproteasomal ubiquitin receptor Dsk2. This complex localizes at promoters of active genes and it is required for transcription. The functions played by the different components of the HP1c complex are not fully understood. In this study we show that WOC and ROW are required for chromatin binding of both Dsk2 and HP1c. However, while impairing chromatin binding strongly destabilizes HP1c, it does not affect Dsk2 stability. We also show that WOC, but not ROW, is required for nuclear localization of Dsk2. Moreover, WOC and Dsk2 co-immunoprecitate upon ROW depletion. These results suggest that WOC and Dsk2 interact to form a subcomplex that mediates nuclear translocation of Dsk2. We also show that ROW mediates chromatin binding of the WOC/Dsk2 subcomplex, as well as of HP1c. Altogether these observations favor a model by which the interaction with WOC recruits Dsk2 to the HP1c complex that, in its turn, binds chromatin in a ROW-dependent manner.
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Affiliation(s)
- Gianmarco Di Mauro
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Albert Carbonell
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Paula Escudero-Ferruz
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain.
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24
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Izumikawa K, Ishikawa H, Yoshikawa H, Fujiyama S, Watanabe A, Aburatani H, Tachikawa H, Hayano T, Miura Y, Isobe T, Simpson RJ, Li L, Min J, Takahashi N. LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA. Nucleic Acids Res 2019; 47:10357-10372. [PMID: 31504794 PMCID: PMC6821171 DOI: 10.1093/nar/gkz747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/22/2019] [Accepted: 08/20/2018] [Indexed: 02/06/2023] Open
Abstract
Activation of ribosomal RNA (rRNA) synthesis is pivotal during cell growth and proliferation, but its aberrant upregulation may promote tumorigenesis. Here, we demonstrate that the candidate oncoprotein, LYAR, enhances ribosomal DNA (rDNA) transcription. Our data reveal that LYAR binds the histone-associated protein BRD2 without involvement of acetyl-lysine-binding bromodomains and recruits BRD2 to the rDNA promoter and transcribed regions via association with upstream binding factor. We show that BRD2 is required for the recruitment of the MYST-type acetyltransferase KAT7 to rDNA loci, resulting in enhanced local acetylation of histone H4. In addition, LYAR binds a complex of BRD4 and KAT7, which is then recruited to rDNA independently of the BRD2-KAT7 complex to accelerate the local acetylation of both H4 and H3. BRD2 also helps recruit BRD4 to rDNA. By contrast, LYAR has no effect on rDNA methylation or the binding of RNA polymerase I subunits to rDNA. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.
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Affiliation(s)
- Keiichi Izumikawa
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hideaki Ishikawa
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Harunori Yoshikawa
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sally Fujiyama
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Akira Watanabe
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University 53, Shogoin-kawahara-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-8507, Japan
| | - Hiroyuki Aburatani
- Laboratory for System Biology and Medicine, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroyuki Tachikawa
- Department of Applied Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Hayano
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Japan
| | - Yutaka Miura
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Richard J Simpson
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,La Trobe Institute for Molecular Science (LIMS) LIMS Building 1, Room 412 La Trobe University, Bundoora Victoria 3086, Australia
| | - Li Li
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jinrong Min
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nobuhiro Takahashi
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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25
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Critical role for TRIM28 and HP1β/γ in the epigenetic control of T cell metabolic reprograming and effector differentiation. Proc Natl Acad Sci U S A 2019; 116:25839-25849. [PMID: 31776254 PMCID: PMC6925996 DOI: 10.1073/pnas.1901639116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
CD4 T cells are major regulators of immune responses against both self and pathogens. Understanding pathways that govern CD4 T cell differentiation and regulation are thus key for the discovery of new immunoregulatory drug targets. Here, we have identified an epigenetic pathway that regulates the expression of a set of proteins that determine T cell responsiveness. By silencing enhancers distal to a set of genes known to be involved in regulatory T cell function, the epigenetic modifiers TRIM28 and HP1β/γ regulate T cell receptor signaling. This leads to defective metabolic reprograming and inefficient effector differentiation of naive T cells. This mechanism provides an exciting opportunity to regulate T cell responsivity in both autoimmunity and T cell-based immunodeficiencies. Naive CD4+ T lymphocytes differentiate into different effector types, including helper and regulatory cells (Th and Treg, respectively). Heritable gene expression programs that define these effector types are established during differentiation, but little is known about the epigenetic mechanisms that install and maintain these programs. Here, we use mice defective for different components of heterochromatin-dependent gene silencing to investigate the epigenetic control of CD4+ T cell plasticity. We show that, upon T cell receptor (TCR) engagement, naive and regulatory T cells defective for TRIM28 (an epigenetic adaptor for histone binding modules) or for heterochromatin protein 1 β and γ isoforms (HP1β/γ, 2 histone-binding factors involved in gene silencing) fail to effectively signal through the PI3K–AKT–mTOR axis and switch to glycolysis. While differentiation of naive TRIM28−/− T cells into cytokine-producing effector T cells is impaired, resulting in reduced induction of autoimmune colitis, TRIM28−/− regulatory T cells also fail to expand in vivo and to suppress autoimmunity effectively. Using a combination of transcriptome and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses for H3K9me3, H3K9Ac, and RNA polymerase II, we show that reduced effector differentiation correlates with impaired transcriptional silencing at distal regulatory regions of a defined set of Treg-associated genes, including, for example, NRP1 or Snai3. We conclude that TRIM28 and HP1β/γ control metabolic reprograming through epigenetic silencing of a defined set of Treg-characteristic genes, thus allowing effective T cell expansion and differentiation into helper and regulatory phenotypes.
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26
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DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1β-Ser88. Cells 2019; 8:cells8091097. [PMID: 31533340 PMCID: PMC6770535 DOI: 10.3390/cells8091097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 12/28/2022] Open
Abstract
The family of heterochromatin protein 1 (HP1) isoforms is essential for chromatin packaging, regulation of gene expression, and repair of damaged DNA. Here we document that γ-radiation reduced the number of HP1α-positive foci, but not HP1β and HP1γ foci, located in the vicinity of the fibrillarin-positive region of the nucleolus. The additional analysis confirmed that γ-radiation has the ability to significantly decrease the level of HP1α in rDNA promoter and rDNA encoding 28S rRNA. By mass spectrometry, we showed that treatment by γ-rays enhanced the HP1β serine 88 phosphorylation (S88ph), but other analyzed modifications of HP1β, including S161ph/Y163ph, S171ph, and S174ph, were not changed in cells exposed to γ-rays or treated by the HDAC inhibitor (HDACi). Interestingly, a combination of HDACi and γ-radiation increased the level of HP1α and HP1γ. The level of HP1β remained identical before and after the HDACi/γ-rays treatment, but HDACi strengthened HP1β interaction with the KRAB-associated protein 1 (KAP1) protein. Conversely, HP1γ did not interact with KAP1, although approximately 40% of HP1γ foci co-localized with accumulated KAP1. Especially HP1γ foci at the periphery of nucleoli were mostly absent of KAP1. Together, DNA damage changed the morphology, levels, and interaction properties of HP1 isoforms. Also, γ-irradiation-induced hyperphosphorylation of the HP1β protein; thus, HP1β-S88ph could be considered as an important marker of DNA damage.
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27
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Crawford NT, McIntyre AJ, McCormick A, D'Costa ZC, Buckley NE, Mullan PB. TBX2 interacts with heterochromatin protein 1 to recruit a novel repression complex to EGR1-targeted promoters to drive the proliferation of breast cancer cells. Oncogene 2019; 38:5971-5986. [PMID: 31253870 DOI: 10.1038/s41388-019-0853-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 11/09/2022]
Abstract
Early Growth Response 1 (EGR1) is a stress response transcription factor with multiple tumour suppressor roles in breast tissue, whose expression is often lost in breast cancers. We have previously shown that the breast cancer oncogene TBX2 (T-BOX2) interacts with EGR1 to co-repress EGR1-target genes including the breast tumour suppressor NDRG1. Here, we show the mechanistic basis of this TBX2 repression complex. We show that siRNA knockdown of TBX2, EGR1, Heterochromatin Protein 1 (HP1) isoforms and the generic HP1-associated corepressor protein KAP1 all resulted in growth inhibition of TBX2-expressing breast cancer cells. We show that TBX2 interacts with HP1 through a conserved HP1-binding motif in its N-terminus, which in turn leads to the recruitment of KAP1 and other associated proteins. Mutation of the TBX2 HP1 binding domain abrogates the TBX2-HP1 interaction and loss of repression of target genes such as NDRG1. Chromatin-immunoprecipitation (ChIP) assays showed that TBX2 establishes a repressive chromatin mark, specifically H3K9me3, around the NDRG1 proximal promoter coincident with the recruitment of the DNA methyltransferase DNMT3B and histone methyltransferase (HMT) complex components (G9A, Enhancer of Zeste 2 (EZH2) and Suppressor of Zeste 12 (SUZ12)). Knockdown of G9A, EZH2 or SUZ12 resulted in upregulation of TBX2/EGR1 co-regulated targets accompanied by a dramatic inhibition of cell proliferation. We show that a generic inhibitor of HMT activity, DzNep, phenocopies expression of an inducible dominant negative TBX2. Knockdown of TBX2, KAP1 or HP1 inhibited NDRG1 promoter decoration specifically with the H3K9me3 repression mark. Correspondingly, treatment with a G9A inhibitor effectively reversed TBX2 repression of NDRG1 and synergistically downregulated cell proliferation following TBX2 functional inhibition. These data demonstrate that TBX2 promotes suppression of normal growth control mechanisms through recruitment of a large repression complex to EGR1-responsive promoters leading to the uncontrolled proliferation of breast cancer cells.
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Affiliation(s)
- N T Crawford
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - A J McIntyre
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - A McCormick
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Z C D'Costa
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - N E Buckley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - P B Mullan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK.
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28
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Rani R, Yaseen AM, Malwade A, Sevilimedu A. An RNA aptamer to HP1/Swi6 facilitates heterochromatin formation at an ectopic locus in S.pombe. RNA Biol 2019; 16:742-753. [PMID: 30794054 DOI: 10.1080/15476286.2019.1584026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe (S.pombe), heterochromatin domains are established and maintained by protein complexes that contain numerous RNA binding domains among their components. The fission yeast HP1 protein Swi6 is one such component and contains an unstructured RNA-binding hinge, which is important for the integrity and silencing of heterochromatin. In this study, we have used an RNA aptamer that likely binds to the Swi6 hinge with high affinity, as a tool to perturb the natural interactions mediated by this domain. When the hinge is blocked by the aptamer RNA, Swi6 appears to become less restricted to the pericentromeres and is enriched at specific euchromatic loci. This suggests a role for the Swi6 hinge, along with the chromoshadow domain (previously shown) in controlling the spread of heterochromatin in S.pombe. The study also highlights the potential of using a synthetic aptamer RNA as a tool to perturb nucleic acid - protein interaction in vivo with the objective of understanding the functional relevance of such an interaction.
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Affiliation(s)
- Rita Rani
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Abdul Mohd Yaseen
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Akshay Malwade
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Aarti Sevilimedu
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
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29
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Heterochromatin protein 1 (HP1) is intrinsically required for post-transcriptional regulation of Drosophila Germline Stem Cell (GSC) maintenance. Sci Rep 2019; 9:4372. [PMID: 30867469 PMCID: PMC6416348 DOI: 10.1038/s41598-019-40152-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/07/2019] [Indexed: 01/05/2023] Open
Abstract
A very important open question in stem cells regulation is how the fine balance between GSCs self-renewal and differentiation is orchestrated at the molecular level. In the past several years much progress has been made in understanding the molecular mechanisms underlying intrinsic and extrinsic controls of GSC regulation but the complex gene regulatory networks that regulate stem cell behavior are only partially understood. HP1 is a dynamic epigenetic determinant mainly involved in heterochromatin formation, epigenetic gene silencing and telomere maintenance. Furthermore, recent studies have revealed the importance of HP1 in DNA repair, sister chromatid cohesion and, surprisingly, in positive regulation of gene expression. Here, we show that HP1 plays a crucial role in the control of GSC homeostasis in Drosophila. Our findings demonstrate that HP1 is required intrinsically to promote GSC self-renewal and progeny differentiation by directly stabilizing the transcripts of key genes involved in GSCs maintenance.
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30
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Kat6b Modulates Oct4 and Nanog Binding to Chromatin in Embryonic Stem Cells and Is Required for Efficient Neural Differentiation. J Mol Biol 2019; 431:1148-1159. [DOI: 10.1016/j.jmb.2019.02.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 11/21/2022]
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31
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Lee DH, Ryu HW, Kim GW, Kwon SH. Comparison of three heterochromatin protein 1 homologs in Drosophila. J Cell Sci 2019; 132:jcs.222729. [PMID: 30659116 DOI: 10.1242/jcs.222729] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/22/2018] [Indexed: 01/20/2023] Open
Abstract
Heterochromatin protein 1 (HP1) is an epigenetic regulator of chromatin structure and genome function in eukaryotes. Despite shared features, most eukaryotes have a minimum of three HP1 homologs with differential localization patterns and functions. Most studies focus on Drosophila HP1a [also known as Su(var)205], and little is known about the properties of HP1b and HP1c. To determine the features of the three HP1 homologs, we performed the first comprehensive comparative analysis of Drosophila HP1 homologs. HP1 differentially homodimerizes and heterodimerizes in vivo and in vitro HP1b and HP1c, but not HP1a, are localized to both the nucleus and cytoplasm. The C-terminal extension region (CTE) targets HP1c and HP1b to the cytoplasm. Biochemical approaches show that HP1 binds to various interacting partners with different binding affinities. Each HP1 associates differently with RNA polymerase II; a gene reporter assay revealed that HP1a and HP1b, but not HP1c, inhibit transcriptional activity, suggesting that HP1c serves as a positive regulator in transcription. Thus, these studies provide the basic clues pertaining to the molecular mechanism by which HP1 might control cellular processes in a homolog-specific manner.
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Affiliation(s)
- Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyun Wook Ryu
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea .,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Republic of Korea
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32
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Akram S, Yang F, Li J, Adams G, Liu Y, Zhuang X, Chu L, Liu X, Emmett N, Thompson W, Mullen M, Muthusamy S, Wang W, Mo F, Liu X. LRIF1 interacts with HP1α to coordinate accurate chromosome segregation during mitosis. J Mol Cell Biol 2018; 10:527-538. [PMID: 30016453 PMCID: PMC6304163 DOI: 10.1093/jmcb/mjy040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/05/2018] [Accepted: 07/14/2018] [Indexed: 01/26/2023] Open
Abstract
Heterochromatin protein 1α (HP1α) regulates chromatin specification and plasticity during cell fate decision. Different structural determinants account for HP1α localization and function during cell division cycle. Our earlier study showed that centromeric localization of HP1α depends on the epigenetic mark H3K9me3 in interphase, while its centromeric location in mitosis relies on uncharacterized PXVXL-containing factors. Here, we identified a PXVXL-containing protein, ligand-dependent nuclear receptor-interacting factor 1 (LRIF1), which recruits HP1α to the centromere of mitotic chromosomes and its interaction with HP1α is essential for accurate chromosome segregation during mitosis. LRIF1 interacts directly with HP1α chromoshadow domain via an evolutionarily conserved PXVXL motif within its C-terminus. Importantly, the LRIF1-HP1α interaction is critical for Aurora B activity in the inner centromere. Mutation of PXVXL motif of LRIF1 leads to defects in HP1α centromere targeting and aberrant chromosome segregation. These findings reveal a previously unrecognized direct link between LRIF1 and HP1α in centromere plasticity control and illustrate the critical role of LRIF1-HP1α interaction in orchestrating accurate cell division.
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Affiliation(s)
- Saima Akram
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
| | - Fengrui Yang
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Junying Li
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
| | - Gregory Adams
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
- National Institutes of Health, Bethesda, MD, USA
| | - Yingying Liu
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Xiaoxuan Zhuang
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- National Institutes of Health, Bethesda, MD, USA
| | - Lingluo Chu
- Department of Molecular Cell Biology, Harvard University, Cambridge, MA, USA
| | - Xu Liu
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Nerimah Emmett
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Winston Thompson
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - McKay Mullen
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Saravana Muthusamy
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Wenwen Wang
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Fei Mo
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- National Institutes of Health, Bethesda, MD, USA
| | - Xing Liu
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
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33
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RNA polymerase II pausing and transcriptional regulation of the HSP70 expression. Eur J Cell Biol 2017; 96:739-745. [DOI: 10.1016/j.ejcb.2017.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 08/16/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022] Open
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34
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Lakhotia SC. Non-coding RNAs demystify constitutive heterochromatin as essential modulator of epigenotype. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0221-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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35
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Hyun K, Jeon J, Park K, Kim J. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017; 49:e324. [PMID: 28450737 PMCID: PMC6130214 DOI: 10.1038/emm.2017.11] [Citation(s) in RCA: 676] [Impact Index Per Article: 96.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 02/08/2023] Open
Abstract
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
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Affiliation(s)
- Kwangbeom Hyun
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongcheol Jeon
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kihyun Park
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jaehoon Kim
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Boldyreva LV, Goncharov FP, Demakova OV, Zykova TY, Levitsky VG, Kolesnikov NN, Pindyurin AV, Semeshin VF, Zhimulev IF. Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines. Curr Genomics 2017; 18:214-226. [PMID: 28367077 PMCID: PMC5345337 DOI: 10.2174/1389202917666160512164913] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. RESULTS Here, we describe the properties of these chromatin types across different cell lines. We show that aquamarine chromatin tends to harbor transcription start sites (TSSs) and 5' untranslated regions (5'UTRs) of the genes, is enriched in diverse "open" chromatin proteins, histone modifications, nucleosome remodeling complexes and transcription factors. It encompasses most of the tRNA genes and shows enrichment for non-coding RNAs and miRNA genes. Lazurite chromatin typically encompasses gene bodies. It is rich in proteins involved in transcription elongation. Frequency of both point mutations and natural deletion breakpoints is elevated within lazurite chromatin. Malachite chromatin shows higher frequency of insertions of natural transposons. Finally, ruby chromatin is enriched for proteins and histone modifications typical for the "closed" chromatin. Ruby chromatin has a relatively low frequency of point mutations and is essentially devoid of miRNA and tRNA genes. Aquamarine and ruby chromatin types are highly stable across cell lines and have contrasting properties. Lazurite and malachite chromatin types also display characteristic protein composition, as well as enrichment for specific genomic features. We found that two types of chromatin, aquamarine and ruby, retain their complementary protein patterns in four Drosophila cell lines.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Igor F. Zhimulev
- Address correspondence to this author at the Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Tel: +7 383 363-90-41; Fax: +7 383 363-90-78; E-mail:
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Huang C, Su T, Xue Y, Cheng C, Lay FD, McKee RA, Li M, Vashisht A, Wohlschlegel J, Novitch BG, Plath K, Kurdistani SK, Carey M. Cbx3 maintains lineage specificity during neural differentiation. Genes Dev 2017; 31:241-246. [PMID: 28270516 PMCID: PMC5358721 DOI: 10.1101/gad.292169.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/27/2017] [Indexed: 02/05/2023]
Abstract
Chromobox homolog 3 (Cbx3/heterochromatin protein 1γ [HP1γ]) stimulates cell differentiation, but its mechanism is unknown. We found that Cbx3 binds to gene promoters upon differentiation of murine embryonic stem cells (ESCs) to neural progenitor cells (NPCs) and recruits the Mediator subunit Med26. RNAi knockdown of either Cbx3 or Med26 inhibits neural differentiation while up-regulating genes involved in mesodermal lineage decisions. Thus, Cbx3 and Med26 together ensure the fidelity of lineage specification by enhancing the expression of neural genes and down-regulating genes specific to alternative fates.
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Affiliation(s)
- Chengyang Huang
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
- Department of Neurobiology, Shantou University Medical College, Shantou 515041, China
| | - Trent Su
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Yong Xue
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Chen Cheng
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Fides D Lay
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Robin A McKee
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Meiyang Li
- Department of Neurobiology, Shantou University Medical College, Shantou 515041, China
| | - Ajay Vashisht
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Bennett G Novitch
- Department of Neurobiology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Michael Carey
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
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Eguchi T, Calderwood SK, Takigawa M, Kubota S, Kozaki KI. Intracellular MMP3 Promotes HSP Gene Expression in Collaboration With Chromobox Proteins. J Cell Biochem 2016; 118:43-51. [PMID: 27206651 DOI: 10.1002/jcb.25607] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 12/12/2022]
Abstract
Matrix metalloproteinases (MMPs) are crucial factors in tumor progression, inflammatory/immune responses and tissue development/regeneration. Of note, it has been known that MMPs promote genome instability, epithelial-mesenchymal transition, invasion, and metastasis in tumor progression. We previously reported that human MMP3 could translocate into cellular nuclei and control transcription in human chondrosarcoma-derived cells and in articular cartilage (Eguchi et al. [2008] Mol Cell Biol 28(7):2391-2413); however, further transcriptional target genes and cofactors of intranuclear MMP3 have not been uncovered. In this paper, we used transcriptomics analysis in order to examine novel transcriptional target genes regulated by intracellular MMP3. We found that mRNA levels of HSP family members (HSP70B', HSP72, HSP40/DNAJ, and HSP20/CRYAB) are upregulated by the intracellular MMP3 overload. Bioinformatic analysis predicted several transcription factors that possibly interact with MMP3. Among these factors, heat shock factor 1 (HSF1) cooperated with the MMP3 to activate the HSP70B' gene promoter in reporter gene assays, while a dominant negative HSF1 blocked the role for MMP3 in the trans-activation. The hemopexin-like repeat (PEX) domain of the human MMP3 was essential for transcriptional induction of the HSP70B' gene. In addition, chromobox proteins CBX5/HP1α and CBX3/HP1γ cooperated with the PEX domain in induction of HSP70B' mRNA. Taken together, this study newly clarified that intracellular MMP3 cooperate with CBXs/HP1s in transcriptional promotion of HSP genes. J. Cell. Biochem. 118: 43-51, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Takanori Eguchi
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02115, Massachusetts.,Department of Dental Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8525, Japan.,Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School/Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8525, Japan.,Department of Oral Disease Research, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02115, Massachusetts
| | - Masaharu Takigawa
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School/Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8525, Japan
| | - Satoshi Kubota
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8525, Japan
| | - Ken-Ichi Kozaki
- Department of Dental Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8525, Japan
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Abstract
The proto-oncogene c-Jun plays crucial roles in tumorigenesis, and its aberrant expression has been implicated in many cancers. Previous studies have shown that the c-Jun gene is positively autoregulated by its product. Notably, it has also been reported that c-Jun proteins are enriched in its gene body region. However, the role of c-Jun proteins in its gene body region has yet to be uncovered. HP1a is an evolutionarily conserved heterochromatin-associated protein, which plays an essential role in heterochromatin-mediated gene silencing. Interestingly, accumulating evidence shows that HP1a is also localized to euchromatic regions to positively regulate gene transcription. However, the underlying mechanism has not been defined. In this study, we demonstrate that HP1a is involved in the positive autoregulatory loop of the Jra gene, the c-Jun homolog in Drosophila. Jra recruits the HP1a/KDM4A complex to its gene body region upon osmotic stress to reduce H3K36 methylation levels and disrupt H3K36 methylation-dependent histone deacetylation, resulting in high levels of histone acetylation in the Jra gene body region, thus promoting gene transcription. These results not only expand our knowledge toward the mechanism of c-Jun regulation, but also reveal the mechanism by which HP1a exerts its positive regulatory function in gene expression.
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Affiliation(s)
- Yan Liu
- a College of Life Sciences; Hebei United University ; Tangshan , China
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40
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Bártová E, Večeřa J, Krejčí J, Legartová S, Pacherník J, Kozubek S. The level and distribution pattern of HP1β in the embryonic brain correspond to those of H3K9me1/me2 but not of H3K9me3. Histochem Cell Biol 2016; 145:447-61. [PMID: 26794325 DOI: 10.1007/s00418-015-1402-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 01/13/2023]
Abstract
We studied the histone signature of embryonic and adult brains to strengthen existing evidence of the importance of the histone code in mouse brain development. We analyzed the levels and distribution patterns of H3K9me1, H3K9me2, H3K9me3, and HP1β in both embryonic and adult brains. Western blotting showed that during mouse brain development, the levels of H3K9me1, H3K9me2, and HP1β exhibited almost identical trends, with the highest protein levels occurring at E15 stage. These trends differed from the relatively stable level of H3K9me3 at developmental stages E8, E13, E15, and E18. Compared with embryonic brains, adult brains were characterized by very low levels of H3K9me1/me2/me3 and HP1β. Manipulation of the embryonic epigenome through histone deacetylase inhibitor treatment did not affect the distribution patterns of the studied histone markers in embryonic ventricular ependyma. Similarly, Hdac3 depletion in adult animals had no effect on histone methylation in the adult hippocampus. Our results indicate that the distribution of HP1β in the embryonic mouse brain is related to that of H3K9me1/me2 but not to that of H3K9me3. The unique status of H3K9me3 in the brain was confirmed by its pronounced accumulation in the granular layer of the adult olfactory bulb. Moreover, among the studied proteins, H3K9me3 was the only posttranslational histone modification that was highly abundant at clusters of centromeric heterochromatin, called chromocenters. When we focused on the hippocampus, we found this region to be rich in H3K9me1 and H3K9me3, whereas H3K9me2 and HP1β were present at a very low level or even absent in the hippocampal blade. Taken together, these results revealed differences in the epigenome of the embryonic and adult mouse brain and showed that the adult hippocampus, the granular layer of the adult olfactory bulb, and the ventricular ependyma of the embryonic brain are colonized by specific epigenetic marks.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic.
| | - Josef Večeřa
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Jana Krejčí
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jiří Pacherník
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
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Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-98. [PMID: 26034889 DOI: 10.1146/annurev-biochem-060614-034242] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays a pivotal role in the flow of genetic information from DNA to proteins by expanding the coding capacity of genomes. Regulation of alternative splicing is as important as regulation of transcription to determine cell- and tissue-specific features, normal cell functioning, and responses of eukaryotic cells to external cues. Its importance is confirmed by the evolutionary conservation and diversification of alternative splicing and the fact that its deregulation causes hereditary disease and cancer. This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in which chromatin structure, DNA methylation, histone marks, and nucleosome positioning play a fundamental role in providing a dynamic scaffold for interactions between the splicing and transcription machineries. We focus on evidence for how the kinetics of RNA polymerase II (RNAPII) elongation and the recruitment of splicing factors and adaptor proteins to chromatin components act in coordination to regulate alternative splicing.
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Affiliation(s)
- Shiran Naftelberg
- Sackler Medical School, Tel Aviv University, Tel Aviv 69978, Israel;
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42
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Bondarenko MT, Maluchenko NV, Valieva ME, Gerasimova NS, Kulaeva OI, Georgiev PG, Studitsky VM. Structure and function of histone chaperone FACT. Mol Biol 2015. [DOI: 10.1134/s0026893315060023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells. Genome Biol 2015; 16:213. [PMID: 26415775 PMCID: PMC4587738 DOI: 10.1186/s13059-015-0760-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/25/2015] [Indexed: 11/22/2022] Open
Abstract
Background Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. Results Here we identify Heterochromatin Protein 1β (HP1β) as an essential protein for proper differentiation, and, unexpectedly, for the maintenance of pluripotency in ESCs. In pluripotent and differentiated cells HP1β is differentially localized and differentially associated with chromatin. Deletion of HP1β, but not HP1α, in ESCs provokes a loss of the morphological and proliferative characteristics of embryonic pluripotent cells, reduces expression of pluripotency factors and causes aberrant differentiation. However, in differentiated cells, loss of HP1β has the opposite effect, perturbing maintenance of the differentiation state and facilitating reprogramming to an induced pluripotent state. Microscopy, biochemical fractionation and chromatin immunoprecipitation reveal a diffuse nucleoplasmic distribution, weak association with chromatin and high expression levels for HP1β in ESCs. The minor fraction of HP1β that is chromatin-bound in ESCs is enriched within exons, unlike the situation in differentiated cells, where it binds heterochromatic satellite repeats and chromocenters. Conclusions We demonstrate an unexpected duality in the role of HP1β: it is essential in ESCs for maintaining pluripotency, while it is required for proper differentiation in differentiated cells. Thus, HP1β function both depends on, and regulates, the pluripotent state. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0760-8) contains supplementary material, which is available to authorized users.
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Bunch H, Calderwood SK. TRIM28 as a novel transcriptional elongation factor. BMC Mol Biol 2015; 16:14. [PMID: 26293668 PMCID: PMC4545989 DOI: 10.1186/s12867-015-0040-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/22/2015] [Indexed: 12/21/2022] Open
Abstract
TRIM28 is a multidomain protein with versatile functions in transcription and DNA repair. Recently it was shown that this factor plays unanticipated roles in transcriptional elongation. TRIM28 was shown to stabilize the pausing of RNA polymerase II (Pol II) close to the transcriptional start site in many unactivated genes, permitting Pol II accumulation and readying genes for induction. In addition, the factor was shown to respond rapidly to signals accompanying transcriptional activation permitting the productive elongation of RNA by previously paused Pol II. We discuss here critical regulatory mechanisms of TRIM28 in transcriptional control and DNA repair that may illuminate the novel roles of this factor in pausing and elongation of Pol II.
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Affiliation(s)
- Heeyoun Bunch
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Center for Life Sciences, 3 Blackfan circle, Boston, MA, 02115, USA.
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Center for Life Sciences, 3 Blackfan circle, Boston, MA, 02115, USA.
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45
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Srivastava R, Ahn SH. Modifications of RNA polymerase II CTD: Connections to the histone code and cellular function. Biotechnol Adv 2015; 33:856-72. [PMID: 26241863 DOI: 10.1016/j.biotechadv.2015.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/08/2015] [Accepted: 07/28/2015] [Indexed: 12/24/2022]
Abstract
At the onset of transcription, many protein machineries interpret the cellular signals that regulate gene expression. These complex signals are mostly transmitted to the indispensable primary proteins involved in transcription, RNA polymerase II (RNAPII) and histones. RNAPII and histones are so well coordinated in this cellular function that each cellular signal is precisely allocated to specific machinery depending on the stage of transcription. The carboxy-terminal domain (CTD) of RNAPII in eukaryotes undergoes extensive posttranslational modification, called the 'CTD code', that is indispensable for coupling transcription with many cellular processes, including mRNA processing. The posttranslational modification of histones, known as the 'histone code', is also critical for gene transcription through the reversible and dynamic remodeling of chromatin structure. Notably, the histone code is closely linked with the CTD code, and their combinatorial effects enable the delicate regulation of gene transcription. This review elucidates recent findings regarding the CTD modifications of RNAPII and their coordination with the histone code, providing integrative pathways for the fine-tuned regulation of gene expression and cellular function.
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Affiliation(s)
- Rakesh Srivastava
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Seong Hoon Ahn
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea.
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46
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dDsk2 regulates H2Bub1 and RNA polymerase II pausing at dHP1c complex target genes. Nat Commun 2015; 6:7049. [PMID: 25916810 DOI: 10.1038/ncomms8049] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 03/26/2015] [Indexed: 12/13/2022] Open
Abstract
dDsk2 is a conserved extraproteasomal ubiquitin receptor that targets ubiquitylated proteins for degradation. Here we report that dDsk2 plays a nonproteolytic function in transcription regulation. dDsk2 interacts with the dHP1c complex, localizes at promoters of developmental genes and is required for transcription. Through the ubiquitin-binding domain, dDsk2 interacts with H2Bub1, a modification that occurs at dHP1c complex-binding sites. H2Bub1 is not required for binding of the complex; however, dDsk2 depletion strongly reduces H2Bub1. Co-depletion of the H2Bub1 deubiquitylase dUbp8/Nonstop suppresses this reduction and rescues expression of target genes. RNA polymerase II is strongly paused at promoters of dHP1c complex target genes and dDsk2 depletion disrupts pausing. Altogether, these results suggest that dDsk2 prevents dUbp8/Nonstop-dependent H2Bub1 deubiquitylation at promoters of dHP1c complex target genes and regulates RNA polymerase II pausing. These results expand the catalogue of nonproteolytic functions of ubiquitin receptors to the epigenetic regulation of chromatin modifications.
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Garrigues JM, Sidoli S, Garcia BA, Strome S. Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. Genome Res 2014; 25:76-88. [PMID: 25467431 PMCID: PMC4317175 DOI: 10.1101/gr.180489.114] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Formation of heterochromatin serves a critical role in organizing the genome and regulating gene expression. In most organisms, heterochromatin flanks centromeres and telomeres. To identify heterochromatic regions in the heavily studied model C. elegans, which possesses holocentric chromosomes with dispersed centromeres, we analyzed the genome-wide distribution of the heterochromatin protein 1 (HP1) ortholog HPL-2 and compared its distribution to other features commonly associated with heterochromatin. HPL-2 binding highly correlates with histone H3 mono- and dimethylated at lysine 9 (H3K9me1 and H3K9me2) and forms broad domains on autosomal arms. Although HPL-2, like other HP1 orthologs, binds H3K9me peptides in vitro, the distribution of HPL-2 in vivo appears relatively normal in mutant embryos that lack H3K9me, demonstrating that the chromosomal distribution of HPL-2 can be achieved in an H3K9me-independent manner. Consistent with HPL-2 serving roles independent of H3K9me, hpl-2 mutant worms display more severe defects than mutant worms lacking H3K9me. HPL-2 binding is enriched for repetitive sequences, and on chromosome arms is anticorrelated with centromeres. At the genic level, HPL-2 preferentially associates with well-expressed genes, and loss of HPL-2 results in up-regulation of some binding targets and down-regulation of others. Our work defines heterochromatin in an important model organism and uncovers both shared and distinctive properties of heterochromatin relative to other systems.
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Affiliation(s)
- Jacob M Garrigues
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Simone Sidoli
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Susan Strome
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA;
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Cryderman DE, Vitalini MW, Wallrath LL. Heterochromatin protein 1a is required for an open chromatin structure. Transcription 2014; 2:95-99. [PMID: 21468237 DOI: 10.4161/trns.2.2.14687] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 12/30/2010] [Accepted: 12/31/2010] [Indexed: 01/03/2023] Open
Abstract
The Drosophila melanogaster fourth chromosome contains interspersed domains of active and repressive chromatin. We investigated a stock harboring a silenced transgene inserted into Dyrk3 and near Caps-two expressed genes on chromosome four. In an HP1a-deficient background, transgene expression was activated while, paradoxically, expression of Dyrk3 and Caps was reduced. We found that the promoters of Dyrk3 and Caps contained DNase I hypersensitive sites but also possessed methylated histone H3 and HP1a, marks of repressive chromatin. In HP1a-deficient flies, the Dyrk3 and Caps promoters displayed diminished accessibility to nuclease digestion, revealing a surprising role for HP1a in opening chromatin.
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49
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Alekseyenko AA, Gorchakov AA, Zee BM, Fuchs SM, Kharchenko PV, Kuroda MI. Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs. Genes Dev 2014; 28:1445-60. [PMID: 24990964 PMCID: PMC4083088 DOI: 10.1101/gad.241950.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Heterochromatin protein 1 (HP1a) plays conserved roles in gene silencing and heterochromatin and is also implicated in transcription, DNA replication, and repair. Using BioTAP-XL mass spectrometry and sequencing across multiple life stages of Drosophila, Alekseyenko et al. identify HP1a chromatin-associated protein and RNA interactions. They discover 13 novel candidates among the top interactions. Furthermore, HP1a selectively associates with a broad set of RNAs transcribed from repetitive regions. The validation of several novel HP1a protein interactors reveals new HP1a links to chromatin organization and function. Heterochromatin protein 1 (HP1a) has conserved roles in gene silencing and heterochromatin and is also implicated in transcription, DNA replication, and repair. Here we identify chromatin-associated protein and RNA interactions of HP1a by BioTAP-XL mass spectrometry and sequencing from Drosophila S2 cells, embryos, larvae, and adults. Our results reveal an extensive list of known and novel HP1a-interacting proteins, of which we selected three for validation. A strong novel interactor, dADD1 (Drosophila ADD1) (CG8290), is highly enriched in heterochromatin, harbors an ADD domain similar to human ATRX, displays selective binding to H3K9me2 and H3K9me3, and is a classic genetic suppressor of position-effect variegation. Unexpectedly, a second hit, HIPP1 (HP1 and insulator partner protein-1) (CG3680), is strongly connected to CP190-related complexes localized at putative insulator sequences throughout the genome in addition to its colocalization with HP1a in heterochromatin. A third interactor, the histone methyltransferase MES-4, is also enriched in heterochromatin. In addition to these protein–protein interactions, we found that HP1a selectively associated with a broad set of RNAs transcribed from repetitive regions. We propose that this rich network of previously undiscovered interactions will define how HP1a complexes perform their diverse functions in cells and developing organisms.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andrey A Gorchakov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Institute of Molecular and Cellular Biology, Novosibirsk 630090, Russia
| | - Barry M Zee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stephen M Fuchs
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA; Hematology/Oncology Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Chu L, Huo Y, Liu X, Yao P, Thomas K, Jiang H, Zhu T, Zhang G, Chaudhry M, Adams G, Thompson W, Dou Z, Jin C, He P, Yao X. The spatiotemporal dynamics of chromatin protein HP1α is essential for accurate chromosome segregation during cell division. J Biol Chem 2014; 289:26249-26262. [PMID: 25104354 DOI: 10.1074/jbc.m114.581504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heterochromatin protein 1α (HP1α) is involved in regulation of chromatin plasticity, DNA damage repair, and centromere dynamics. HP1α detects histone dimethylation and trimethylation of Lys-9 via its chromodomain. HP1α localizes to heterochromatin in interphase cells but is liberated from chromosomal arms at the onset of mitosis. However, the structural determinants required for HP1α localization in interphase and the regulation of HP1α dynamics have remained elusive. Here we show that centromeric localization of HP1α depends on histone H3 Lys-9 trimethyltransferase SUV39H1 activity in interphase but not in mitotic cells. Surprisingly, HP1α liberates from chromosome arms in early mitosis. To test the role of this dissociation, we engineered an HP1α construct that persistently localizes to chromosome arms. Interestingly, persistent localization of HP1α to chromosome arms perturbs accurate kinetochore-microtubule attachment due to an aberrant distribution of chromosome passenger complex and Sgo1 from centromeres to chromosome arms that prevents resolution of sister chromatids. Further analyses showed that Mis14 and perhaps other PXVXL-containing proteins are involved in directing localization of HP1α to the centromere in mitosis. Taken together, our data suggest a model in which spatiotemporal dynamics of HP1α localization to centromere is governed by two distinct structural determinants. These findings reveal a previously unrecognized but essential link between HP1α-interacting molecular dynamics and chromosome plasticity in promoting accurate cell division.
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Affiliation(s)
- Lingluo Chu
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Yuda Huo
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Xing Liu
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China,; Departments of Physiology and Morehouse School of Medicine, Atlanta, Georgia 30310
| | - Phil Yao
- Departments of Physiology and Morehouse School of Medicine, Atlanta, Georgia 30310; Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
| | - Kelwyn Thomas
- Departments of Neurobiology, Morehouse School of Medicine, Atlanta, Georgia 30310
| | - Hao Jiang
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Tongge Zhu
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China,; Departments of Physiology and Morehouse School of Medicine, Atlanta, Georgia 30310
| | - Guanglan Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou 510623, China, and
| | - Maryam Chaudhry
- Departments of Physiology and Morehouse School of Medicine, Atlanta, Georgia 30310
| | - Gregory Adams
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China,; Departments of Physiology and Morehouse School of Medicine, Atlanta, Georgia 30310
| | - Winston Thompson
- Departments of Physiology and Morehouse School of Medicine, Atlanta, Georgia 30310
| | - Zhen Dou
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Changjiang Jin
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Ping He
- Guangzhou Women and Children's Medical Center, Guangzhou 510623, China, and.
| | - Xuebiao Yao
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China,; Departments of Physiology and Morehouse School of Medicine, Atlanta, Georgia 30310.
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