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Ge W, Yu C, Li J, Yu Z, Li X, Zhang Y, Liu CP, Li Y, Tian C, Zhang X, Li G, Zhu B, Xu RM. Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase. Nature 2023; 616:176-182. [PMID: 36991118 DOI: 10.1038/s41586-023-05841-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 02/14/2023] [Indexed: 03/31/2023]
Abstract
Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification1-3. The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119ub1) on the nucleosome4, counteracting the ubiquitin E3 ligase activity of Polycomb repressive complex 1 (PRC1)5 to facilitate the correct silencing of genes by Polycomb proteins and safeguard active genes from inadvertent silencing by PRC1 (refs. 6-9). The intricate biological function of PR-DUB requires accurate targeting of H2AK119ub1, but PR-DUB can deubiquitinate monoubiquitinated free histones and peptide substrates indiscriminately; the basis for its exquisite nucleosome-dependent substrate specificity therefore remains unclear. Here we report the cryo-electron microscopy structure of human PR-DUB, composed of BAP1 and ASXL1, in complex with the chromatosome. We find that ASXL1 directs the binding of the positively charged C-terminal extension of BAP1 to nucleosomal DNA and histones H3-H4 near the dyad, an addition to its role in forming the ubiquitin-binding cleft. Furthermore, a conserved loop segment of the catalytic domain of BAP1 is situated near the H2A-H2B acidic patch. This distinct nucleosome-binding mode displaces the C-terminal tail of H2A from the nucleosome surface, and endows PR-DUB with the specificity for H2AK119ub1.
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Affiliation(s)
- Weiran Ge
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cong Yu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyu Yu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaorong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Changlin Tian
- Division of Life Sciences and Anhui Provisional Engineering Laboratory of Peptide Drugs, University of Science and Technology of China, Hefei, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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2
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Vincent JB, Ausió J. MeCP2: latest insights fundamentally change our understanding of its interactions with chromatin and its functional attributes. Bioessays 2021; 43:e2000281. [PMID: 33416207 DOI: 10.1002/bies.202000281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022]
Abstract
Methyl CpG binding protein 2 (MeCP2) was initially isolated as an exclusive reader of DNA methylated at CpG. This recognition site, was subsequently extended to other DNA methylated residues and it has been the persisting dogma that binding to methylated DNA constitutes its physiologically relevant role. As we review here, two very recent papers fundamentally change our understanding of the interactions of this protein with chromatin, as well as its functional attributes. In the first one, the protein has been shown to bind to tri-methylated histone H3 (H3K27me3), providing a hint for what might turn out to be the first described chromodomain-containing protein reader in the animal kingdom, and unequivocally demonstrates the ability of MeCP2 to bind to nonmethylated CpG regions of the genome. The second paper reports how the protein dynamically participates in the formation of constitutive heterochromatin condensates. Histone H3K27me3 is a critical component of this form of chromatin.
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Affiliation(s)
- John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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3
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Arroyave F, Montaño D, Lizcano F. Diabetes Mellitus Is a Chronic Disease that Can Benefit from Therapy with Induced Pluripotent Stem Cells. Int J Mol Sci 2020; 21:ijms21228685. [PMID: 33217903 PMCID: PMC7698772 DOI: 10.3390/ijms21228685] [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: 09/10/2020] [Revised: 10/20/2020] [Accepted: 10/31/2020] [Indexed: 12/17/2022] Open
Abstract
Diabetes mellitus (DM) is one of the main causes of morbidity and mortality, with an increasing incidence worldwide. The impact of DM on public health in developing countries has triggered alarm due to the exaggerated costs of the treatment and monitoring of patients with this disease. Considerable efforts have been made to try to prevent the onset and reduce the complications of DM. However, because insulin-producing pancreatic β-cells progressively deteriorate, many people must receive insulin through subcutaneous injection. Additionally, current therapies do not have consistent results regarding the prevention of chronic complications. Leveraging the approval of real-time continuous glucose monitors and sophisticated algorithms that partially automate insulin infusion pumps has improved glycemic control, decreasing the burden of diabetes management. However, these advances are facing physiologic barriers. New findings in molecular and cellular biology have produced an extraordinary advancement in tissue development for the treatment of DM. Obtaining pancreatic β-cells from somatic cells is a great resource that currently exists for patients with DM. Although this therapeutic option has great prospects for patients, some challenges remain for this therapeutic plan to be used clinically. The purpose of this review is to describe the new techniques in cell biology and regenerative medicine as possible treatments for DM. In particular, this review highlights the origin of induced pluripotent cells (iPSCs) and how they have begun to emerge as a regenerative treatment that may mitigate the pathology of this disease.
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Affiliation(s)
- Felipe Arroyave
- Doctoral Program in Biosciences, Universidad de La Sabana, Chía 250008, CU, Colombia;
| | - Diana Montaño
- Center of Biomedical Investigation (CIBUS), Universidad de La Sabana, Chía 250008, CU, Colombia;
| | - Fernando Lizcano
- Doctoral Program in Biosciences, Universidad de La Sabana, Chía 250008, CU, Colombia;
- Center of Biomedical Investigation (CIBUS), Universidad de La Sabana, Chía 250008, CU, Colombia;
- Correspondence: ; Tel.: +57-3144120052 or +57-18615555 (ext. 23906)
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4
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The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:306-327. [PMID: 29309830 DOI: 10.1016/j.pnpbp.2017.12.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/13/2022]
Abstract
The complexity of the human brain emerges from a long and finely tuned developmental process orchestrated by the crosstalk between genome and environment. Vis à vis other species, the human brain displays unique functional and morphological features that result from this extensive developmental process that is, unsurprisingly, highly vulnerable to both genetically and environmentally induced alterations. One of the most striking outcomes of the recent surge of sequencing-based studies on neurodevelopmental disorders (NDDs) is the emergence of chromatin regulation as one of the two domains most affected by causative mutations or Copy Number Variations besides synaptic function, whose involvement had been largely predicted for obvious reasons. These observations place chromatin dysfunction at the top of the molecular pathways hierarchy that ushers in a sizeable proportion of NDDs and that manifest themselves through synaptic dysfunction and recurrent systemic clinical manifestation. Here we undertake a conceptual investigation of chromatin dysfunction in NDDs with the aim of systematizing the available evidence in a new framework: first, we tease out the developmental vulnerabilities in human corticogenesis as a structuring entry point into the causation of NDDs; second, we provide a much needed clarification of the multiple meanings and explanatory frameworks revolving around "epigenetics", highlighting those that are most relevant for the analysis of these disorders; finally we go in-depth into paradigmatic examples of NDD-causing chromatin dysregulation, with a special focus on human experimental models and datasets.
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5
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Gibson MD, Gatchalian J, Slater A, Kutateladze TG, Poirier MG. PHF1 Tudor and N-terminal domains synergistically target partially unwrapped nucleosomes to increase DNA accessibility. Nucleic Acids Res 2017; 45:3767-3776. [PMID: 28082396 PMCID: PMC5397176 DOI: 10.1093/nar/gkw1320] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/20/2016] [Indexed: 01/17/2023] Open
Abstract
The Tudor domain of human PHF1 recognizes trimethylated lysine 36 on histone H3 (H3K36me3). PHF1 relies on this interaction to regulate PRC2 methyltransferase activity, localize to DNA double strand breaks and mediate nucleosome accessibility. Here, we investigate the impact of the PHF1 N-terminal domain (NTD) on the Tudor domain interaction with the nucleosome. We show that the NTD is partially ordered when it is natively attached to the Tudor domain. Through a combination of FRET and single molecule studies, we find that the increase of DNA accessibility within the H3K36me3-containing nucleosome, instigated by the Tudor binding to H3K36me3, is dramatically enhanced by the NTD. We demonstrate that this nearly order of magnitude increase is due to preferential binding of PHF1 to partially unwrapped nucleosomes, and that PHF1 alters DNA–protein binding within the nucleosome by decreasing dissociation rates. These results highlight the potency of a PTM-binding protein to regulate DNA accessibility and underscores the role of the novel mechanism by which nucleosomes control DNA–protein binding through increasing protein dissociation rates.
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Affiliation(s)
- Matthew D Gibson
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Jovylyn Gatchalian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Andrew Slater
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Michael G Poirier
- Department of Physics, Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
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6
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Tao BB, Liu XQ, Zhang W, Li S, Dong D, Xiao M, Zhong J. Evidence for the association of chromatin and microRNA regulation in the human genome. Oncotarget 2017; 8:70958-70966. [PMID: 29050335 PMCID: PMC5642610 DOI: 10.18632/oncotarget.20214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/29/2017] [Indexed: 12/18/2022] Open
Abstract
Both microRNAs (miRNAs) and chromatin regulation play important roles in cellular processes and they function at different regulatory levels of transcription. Although efforts have been devoted to the investigation of miRNA and chromatin regulation, there's still no comprehensive work to illustrate their relationships due tothe lack of whole-genome wide datasets in different human cellular contexts. Based on the recently published large-scale epigenetic data, we examined the association between miRNA and epigenetic machinery. Our work confirmed a general relationship between miRNA biogenesis and chromatin features around pre-miRNA genomic regions. Obvious enrichments of DNA methylation and several histone modifications were observed within the pre-miRNA genomic region, which werecorrelated with miRNA expression levels. Furthermore, chromatin features at genepromoter regionsweretightly associated with miRNA regulation. Interestingly, we found that genes with their promoter regions located in the active chromatin state regions tend to have a higher probability to be targeted by miRNAs. This worksuggests that miRNAs and chromatin features are often highly coordinated, which provides a guide to deeply understand the complexity of gene regulation.
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Affiliation(s)
- Bang-Bao Tao
- Department of Neurosurgery, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200092, China
| | - Xi-Qiang Liu
- Department of Hepatobiliary-Pancreatic Surgery, Zhejiang Provincial People’s Hospital, Hangzhou 310014, China
| | - Wenhao Zhang
- Department of Hematology, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200092, China
| | - Shu Li
- Department of Pathophysiology, Wannan Medical College, Wuhu 241002, China
| | - Dong Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Mang Xiao
- Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310027, China
| | - Jun Zhong
- Department of Neurosurgery, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200092, China
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7
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Abstract
Identification of molecular interactions is paramount to understanding how cells function. Most available technologies rely on co-purification of a protein of interest and its binding partners. Therefore, they are limited in their ability to detect low-affinity interactions and cannot be applied to proteins that localize to difficult-to-solubilize cellular compartments. In vivo proximity labeling (IPL) overcomes these obstacles by covalently tagging proteins and RNAs based on their proximity in vivo to a protein of interest. In IPL, a heterobifunctional probe comprising a photoactivatable moiety and biotin is recruited by a monomeric streptavidin tag fused to a protein of interest. Following UV irradiation, candidate interacting proteins and RNAs are covalently biotinylated with tight spatial and temporal control and subsequently recovered using biotin as an affinity handle. Here, we describe experimental protocols to discover novel protein-protein and protein-RNA interactions using IPL. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- David B Beck
- Department of Medicine, Columbia University Medical Center, New York, New York
| | - Roberto Bonasio
- Epigenetics Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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8
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Akizu N, García MA, Estarás C, Fueyo R, Badosa C, de la Cruz X, Martínez-Balbás MA. EZH2 regulates neuroepithelium structure and neuroblast proliferation by repressing p21. Open Biol 2016; 6:150227. [PMID: 27248655 PMCID: PMC4852452 DOI: 10.1098/rsob.150227] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/17/2016] [Indexed: 11/12/2022] Open
Abstract
The function of EZH2 as a transcription repressor is well characterized. However, its role during vertebrate development is still poorly understood, particularly in neurogenesis. Here, we uncover the role of EZH2 in controlling the integrity of the neural tube and allowing proper progenitor proliferation. We demonstrate that knocking down the EZH2 in chick embryo neural tubes unexpectedly disrupts the neuroepithelium (NE) structure, correlating with alteration of the Rho pathway, and reduces neural progenitor proliferation. Moreover, we use transcriptional profiling and functional assays to show that EZH2-mediated repression of p21(WAF1/CIP1) contributes to both processes. Accordingly, overexpression of cytoplasmic p21(WAF1/CIP1) induces NE structural alterations and p21(WAF1/CIP1) suppression rescues proliferation defects and partially compensates for the structural alterations and the Rho activity. Overall, our findings describe a new role of EZH2 in controlling the NE integrity in the neural tube to allow proper progenitor proliferation.
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Affiliation(s)
- Naiara Akizu
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - María Alejandra García
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Conchi Estarás
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Raquel Fueyo
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Carmen Badosa
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119, Barcelona 08035, Spain Institut Català per la Recerca i Estudis Avançats (ICREA), Barcelona 08018, Spain
| | - Marian A Martínez-Balbás
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
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9
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Veith N, Ziehr H, MacLeod RAF, Reamon-Buettner SM. Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines. BMC Biotechnol 2016; 16:6. [PMID: 26800878 PMCID: PMC4722726 DOI: 10.1186/s12896-016-0238-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/15/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Recombinant cell lines developed for therapeutic antibody production often suffer instability or lose recombinant protein expression during long-term culture. Heterogeneous gene expression among cell line subclones may result from epigenetic modifications of DNA or histones, the protein component of chromatin. We thus investigated in such cell lines, DNA methylation and the chromatin environment along the human eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) promoter in an antibody protein-expression vector which was integrated into the Chinese hamster ovary (CHO) cell line genome. RESULTS We analyzed four PT1-CHO cell lines which exhibited losses of protein expression at advanced passage number (>P35) growing in adherent conditions and in culture medium with 10 % FCS. These cell lines exhibited different integration sites and transgene copy numbers as determined by fluorescence in situ hybridization (FISH) and quantitative PCR (qPCR), respectively. By qRT-PCR, we analyzed the recombinant mRNA expression and correlated it with DNA methylation and with results from various approaches interrogating the chromatin landscape along the EEF1A1 promoter region. Each PT1-CHO cell line displayed specific epigenetic signatures or chromatin marks correlating with recombinant mRNA expression. The cell line with the lowest recombinant mRNA expression (PT1-1) was characterized by the highest nucleosome occupancy and displayed the lowest enrichment for histone marks associated with active transcription. In contrast, the cell line with the highest recombinant mRNA expression (PT1-55) exhibited the highest numbers of formaldehyde-assisted isolation of regulatory elements (FAIRE)-enriched regions, and was marked by enrichment for histone modifications H3K9ac and H3K9me3. Another cell line with the second highest recombinant mRNA transcription and the most stable protein expression (PT1-7) had the highest enrichments of the histone variants H3.3 and H2A.Z, and the histone modification H3K9ac. A further cell line (PT1-30) scored the highest enrichments for the bivalent marks H3K4me3 and H3K27me3. Finally, DNA methylation made a contribution, but only in the culture medium with reduced FCS or in a different expression vector. CONCLUSIONS Our results suggest that the chromatin state along the EEF1A1 promoter region can help predict recombinant mRNA expression, and thus may assist in selecting desirable clones during cell line development for protein production.
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Affiliation(s)
- Nathalie Veith
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Holger Ziehr
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Roderick A F MacLeod
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany.
| | - Stella Marie Reamon-Buettner
- Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs Strasse 1, 30625, Hannover, Germany.
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10
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Profiling of urinary proteins in Karan Fries cows reveals more than 1550 proteins. J Proteomics 2015; 127:193-201. [PMID: 26021477 DOI: 10.1016/j.jprot.2015.05.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 12/15/2022]
Abstract
Urine is a non-invasive source of biological fluid, which reflects the physiological status of the mammals. We have profiled the cow urinary proteome and analyzed its functional significance. The urine collected from three healthy cows was concentrated by diafiltration (DF) followed by protein extraction using three methods, namely methanol, acetone, and ammonium sulphate (AS) precipitation and Proteo Spin urine concentration kit (PS). The quality of the protein was assessed by two-dimensional gel electrophoresis (2DE). In-gel digestion method revealed more proteins (1191) in comparison to in-solution digestion method (541). Collectively, 938, 606 and 444 proteins were identified in LC-MS/MS after in-gel and in-solution tryptic digestion of proteins prepared by AS, PS and DF methods, respectively resulting in identification of a total of 1564 proteins. Gene ontology (GO) using Panther7.0 grouped the majority of the proteins into cytoplasmic (location), catalytic activity (function), and metabolism (biological processes), while Cytoscape grouped proteins into complement and coagulation cascades; protease inhibitor activity and wound healing. Functional significance of few selected proteins seems to play important role in their physiology. Comparative analysis with human urine revealed 315 overlapping proteins. This study reports for the first time evidence of more than 1550 proteins in urine of healthy cow donors. This article is part of a Special Issue entitled: Proteomics in India.
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11
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Abstract
Heterochromatin contributes to the dynamic range of eukaryotic gene expression. In yeast, its ability to suppress transcription is inversely proportional to activator strength. A recent study reveals that Sir silencing proteins enhance the avidity with which nucleosomes assemble, endowing heterochromatin with both repressive and dynamic characteristics.
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Affiliation(s)
- David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA.
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12
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Popov B, Petrov N. pRb-E2F signaling in life of mesenchymal stem cells: Cell cycle, cell fate, and cell differentiation. Genes Dis 2014; 1:174-187. [PMID: 30258863 PMCID: PMC6150080 DOI: 10.1016/j.gendis.2014.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/14/2014] [Indexed: 02/07/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are multipotent cells that can differentiate into various mesodermal lines forming fat, muscle, bone, and other lineages of connective tissue. MSCs possess plasticity and under special metabolic conditions may transform into cells of unusual phenotypes originating from ecto- and endoderm. After transplantation, MSCs release the humoral factors promoting regeneration of the damaged tissue. During last five years, the numbers of registered clinical trials of MSCs have increased about 10 folds. This gives evidence that MSCs present a new promising resource for cell therapy of the most dangerous diseases. The efficacy of the MSCs therapy is limited by low possibilities to regulate their conversion into cells of damaged tissues that is implemented by the pRb-E2F signaling. The widely accepted viewpoint addresses pRb as ubiquitous regulator of cell cycle and tumor suppressor. However, current publications suggest that basic function of the pRb-E2F signaling in development is to regulate cell fate and differentiation. Through facultative and constitutive chromatin modifications, pRb-E2F signaling promotes transient and stable cells quiescence, cell fate choice to differentiate, to senesce, or to die. Loss of pRb is associated with cancer cell fate. pRb regulates cell fate by retaining quiescence of one cell population in favor of commitment of another or by suppression of genes of different cell phenotype. pRb is the founder member of the "pocket protein" family possessing functional redundancy. Critical increase in the efficacy of the MSCs based cell therapy will depend on precise understanding of various aspects of the pRb-E2F signaling.
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Affiliation(s)
- Boris Popov
- Institute of Cytology, Russian Academy of Sciences, St.Petersburg, 4, Tikhoretsky Av., 194064, Russia
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13
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Englert NA, Luo G, Goldstein JA, Surapureddi S. Epigenetic modification of histone 3 lysine 27: mediator subunit MED25 is required for the dissociation of polycomb repressive complex 2 from the promoter of cytochrome P450 2C9. J Biol Chem 2014; 290:2264-78. [PMID: 25391650 DOI: 10.1074/jbc.m114.579474] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The Mediator complex is vital for the transcriptional regulation of eukaryotic genes. Mediator binds to nuclear receptors at target response elements and recruits chromatin-modifying enzymes and RNA polymerase II. Here, we examine the involvement of Mediator subunit MED25 in the epigenetic regulation of human cytochrome P450 2C9 (CYP2C9). MED25 is recruited to the CYP2C9 promoter through association with liver-enriched HNF4α, and we show that MED25 influences the H3K27 status of the HNF4α binding region. This region was enriched for the activating marker H3K27ac and histone acetyltransferase CREBBP after MED25 overexpression but was trimethylated when MED25 expression was silenced. The epigenetic regulator Polycomb repressive complex (PRC2), which represses expression by methylating H3K27, plays an important role in target gene regulation. Silencing MED25 correlated with increased association of PRC2 not only with the promoter region chromatin but with HNF4α itself. We confirmed the involvement of MED25 for fully functional preinitiation complex recruitment and transcriptional output in vitro. Formaldehyde-assisted isolation of regulatory elements (FAIRE) revealed chromatin conformation changes that were reliant on MED25, indicating that MED25 induced a permissive chromatin state that reflected increases in CYP2C9 mRNA. For the first time, we showed evidence that a functionally relevant human gene is transcriptionally regulated by HNF4α via MED25 and PRC2. CYP2C9 is important for the metabolism of many exogenous chemicals including pharmaceutical drugs as well as endogenous substrates. Thus, MED25 is important for regulating the epigenetic landscape resulting in transcriptional activation of a highly inducible gene, CYP2C9.
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Affiliation(s)
- Neal A Englert
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - George Luo
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Joyce A Goldstein
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Sailesh Surapureddi
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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14
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Herz HM, Morgan M, Gao X, Jackson J, Rickels R, Swanson SK, Florens L, Washburn MP, Eissenberg JC, Shilatifard A. Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling. Science 2014; 345:1065-70. [PMID: 25170156 DOI: 10.1126/science.1255104] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Histone H3 lysine(27)-to-methionine (H3K27M) gain-of-function mutations occur in highly aggressive pediatric gliomas. We established a Drosophila animal model for the pathogenic histone H3K27M mutation and show that its overexpression resembles polycomb repressive complex 2 (PRC2) loss-of-function phenotypes, causing derepression of PRC2 target genes and developmental perturbations. Similarly, an H3K9M mutant depletes H3K9 methylation levels and suppresses position-effect variegation in various Drosophila tissues. The histone H3K9 demethylase KDM3B/JHDM2 associates with H3K9M-containing nucleosomes, and its misregulation in Drosophila results in changes of H3K9 methylation levels and heterochromatic silencing defects. We have established histone lysine-to-methionine mutants as robust in vivo tools for inhibiting methylation pathways that also function as biochemical reagents for capturing site-specific histone-modifying enzymes, thus providing molecular insight into chromatin signaling pathways.
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Affiliation(s)
- Hans-Martin Herz
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Marc Morgan
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Jessica Jackson
- Saint Louis University School of Medicine, Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis, MO, USA
| | - Ryan Rickels
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Selene K Swanson
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA. Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Joel C Eissenberg
- Saint Louis University School of Medicine, Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis, MO, USA
| | - Ali Shilatifard
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.
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15
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Tushir JS, Akbarian S. Chromatin-bound RNA and the neurobiology of psychiatric disease. Neuroscience 2013; 264:131-41. [PMID: 23831425 DOI: 10.1016/j.neuroscience.2013.06.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022]
Abstract
A large, and still rapidly expanding literature on epigenetic regulation in the nervous system has provided fundamental insights into the dynamic regulation of DNA methylation and post-translational histone modifications in the context of neuronal plasticity in health and disease. Remarkably, however, very little is known about the potential role of chromatin-bound RNAs, including many long non-coding transcripts and various types of small RNAs. Here, we provide an overview on RNA-mediated regulation of chromatin structure and function, with focus on histone lysine methylation and psychiatric disease. Examples of recently discovered chromatin-bound long non-coding RNAs important for neuronal health and function include the brain-derived neurotrophic factor antisense transcript (Bdnf-AS) which regulates expression of the corresponding sense transcript, and LOC389023 which is associated with human-specific histone methylation signatures at the chromosome 2q14.1 neurodevelopmental risk locus by regulating expression of DPP10, an auxillary subunit for voltage-gated K(+) channels. We predict that the exploration of chromatin-bound RNA will significantly advance our current knowledge base in neuroepigenetics and biological psychiatry.
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Affiliation(s)
- J S Tushir
- Friedman Brain Institute, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - S Akbarian
- Friedman Brain Institute, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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16
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Brennan DC, Glassock RJ, Bleyer AJ. American Society of Nephrology Quiz and Questionnaire 2012: Transplantation. Clin J Am Soc Nephrol 2013; 8:1267-72. [PMID: 23539230 DOI: 10.2215/cjn.00430113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Presentation of the Nephrology Quiz and Questionnaire has become an annual tradition at the meetings of the American Society of Nephrology. It is a very popular session, as judged by consistently large attendance. Members of the audience test their knowledge and judgment on a series of case-oriented questions prepared and discussed by experts. They can also compare their answers in real time, using audience response devices, to those of program directors of nephrology training programs in the United States, acquired through an Internet-based questionnaire. Topics presented here include fluid and electrolyte disorders, transplantation, and ESRD and dialysis. Cases representing each of these categories, along with single-best-answer questions, were prepared by a panel of experts (Drs. Palmer, Fervenza, Brennan, and Mehrotra, respectively). The correct and incorrect answers were briefly discussed after the audience responses, and the results of the questionnaire were displayed. This article recapitulates the session and reproduces its educational value for a larger audience--that of the readers of the Clinical Journal of the American Society of Nephrology. Have fun.
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Affiliation(s)
- Daniel C Brennan
- Renal Division, Washington University, St. Louis, Missouri 63110-1010, USA.
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17
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Ho AS, Turcan S, Chan TA. Epigenetic therapy: use of agents targeting deacetylation and methylation in cancer management. Onco Targets Ther 2013; 6:223-32. [PMID: 23569385 PMCID: PMC3615839 DOI: 10.2147/ott.s34680] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The emergence of epigenetic mechanisms as key regulators of gene expression has led to dramatic advances in understanding cancer biology. Driven by complex layers that include aberrant DNA methylation and histone modification, epigenetic aberrations have emerged as critical processes that disrupt cellular machinery and homeostasis. Recent discoveries have already translated into successful clinical trials and improved patient care, with several agents approved for hematologic disease and others undergoing study. As the field matures, substantial challenges persist that will require resolution. These include the need to decipher more fully the interplay between the epigenetic and genetic machinery, patient selection and improving treatment efficacy in solid tumors, and optimizing combination therapies to counteract chemoresistance and minimize adverse effects. Here, we review recent progress in epigenetic treatments and consider their implications for future cancer therapy.
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Affiliation(s)
- Allen S Ho
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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18
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Abstract
Long-range interactions between transcription regulatory elements play an important role in gene activation, epigenetic silencing, and chromatin organization. Transcriptional activation or repression of developmentally regulated genes is often accomplished through tissue-specific chromatin architecture and dynamic localization between active transcription factories and repressive Polycomb bodies. However, the mechanisms underlying the structural organization of chromatin and the coordination of physical interactions are not fully understood. Insulators and Polycomb group proteins form highly conserved multiprotein complexes that mediate functional long-range interactions and have proposed roles in nuclear organization. In this review, we explore recent findings that have broadened our understanding of the function of these proteins and provide an integrative model for the roles of insulators in nuclear organization.
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Affiliation(s)
- Kevin Van Bortle
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
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19
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Livernois AM, Graves JAM, Waters PD. The origin and evolution of vertebrate sex chromosomes and dosage compensation. Heredity (Edinb) 2011; 108:50-8. [PMID: 22086077 DOI: 10.1038/hdy.2011.106] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In mammals, birds, snakes and many lizards and fish, sex is determined genetically (either male XY heterogamy or female ZW heterogamy), whereas in alligators, and in many reptiles and turtles, the temperature at which eggs are incubated determines sex. Evidently, different sex-determining systems (and sex chromosome pairs) have evolved independently in different vertebrate lineages. Homology shared by Xs and Ys (and Zs and Ws) within species demonstrates that differentiated sex chromosomes were once homologous, and that the sex-specific non-recombining Y (or W) was progressively degraded. Consequently, genes are left in single copy in the heterogametic sex, which results in an imbalance of the dosage of genes on the sex chromosomes between the sexes, and also relative to the autosomes. Dosage compensation has evolved in diverse species to compensate for these dose differences, with the stringency of compensation apparently differing greatly between lineages, perhaps reflecting the concentration of genes on the original autosome pair that required dosage compensation. We discuss the organization and evolution of amniote sex chromosomes, and hypothesize that dosage insensitivity might predispose an autosome to evolving function as a sex chromosome.
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Affiliation(s)
- A M Livernois
- Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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