1
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Sibai DS, Tremblay MG, Lessard F, Tav C, Sabourin-Félix M, Robinson M, Moss T. TTF1 control of LncRNA synthesis delineates a tumor suppressor pathway directly regulating the ribosomal RNA genes. J Cell Physiol 2024. [PMID: 38764354 DOI: 10.1002/jcp.31303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
The tumor suppressor p14/19ARF regulates ribosomal RNA (rRNA) synthesis by controlling the nucleolar localization of Transcription Termination Factor 1 (TTF1). However, the role played by TTF1 in regulating the rRNA genes and in potentially controlling growth has remained unclear. We now show that TTF1 expression regulates cell growth by determining the cellular complement of ribosomes. Unexpectedly, it achieves this by acting as a "roadblock" to synthesis of the noncoding LncRNA and pRNA that we show are generated from the "Spacer Promoter" duplications present upstream of the 47S pre-rRNA promoter on the mouse and human ribosomal RNA genes. Unexpectedly, the endogenous generation of these noncoding RNAs does not induce CpG methylation or gene silencing. Rather, it acts in cis to suppress 47S preinitiation complex formation and hence de novo pre-rRNA synthesis by a mechanism reminiscent of promoter interference or occlusion. Taken together, our data delineate a pathway from p19ARF to cell growth suppression via the regulation of ribosome biogenesis by noncoding RNAs and validate a key cellular growth law in mammalian cells.
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Affiliation(s)
- Dany S Sibai
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Michel G Tremblay
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Frédéric Lessard
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Christophe Tav
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Marianne Sabourin-Félix
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Mark Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tom Moss
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
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2
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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3
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Tomkuvienė M, Meier M, Ikasalaitė D, Wildenauer J, Kairys V, Klimašauskas S, Manelytė L. Enhanced nucleosome assembly at CpG sites containing an extended 5-methylcytosine analogue. Nucleic Acids Res 2022; 50:6549-6561. [PMID: 35648439 PMCID: PMC9226530 DOI: 10.1093/nar/gkac444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/05/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Methylation of cytosine to 5-methylcytosine (mC) at CpG sites is a prevalent reversible epigenetic mark in vertebrates established by DNA methyltransferases (MTases); the attached methyl groups can alter local structure of DNA and chromatin as well as binding of dedicated proteins. Nucleosome assembly on methylated DNA has been studied extensively, however little is known how the chromatin structure is affected by larger chemical variations in the major groove of DNA. Here, we studied the nucleosome formation in vitro on DNA containing an extended 5mC analog, 5-(6-azidohex-2-ynyl)cytosine (ahyC) installed at biological relevant CpG sites. We found that multiple ahyC residues on 80-Widom and Hsp70 promoter DNA fragments proved compatible with nucleosome assembly. Moreover, unlike mC, ahyC increases the affinity of histones to the DNA, partially altering nucleosome positioning, stability, and the action of chromatin remodelers. Based on molecular dynamics calculations, we suggest that these new features are due to increased DNA flexibility at ahyC-modified sites. Our findings provide new insights into the biophysical behavior of modified DNA and open new ways for directed design of synthetic nucleosomes.
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Affiliation(s)
- Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Markus Meier
- Biochemistry III, University of Regensburg, Regensburg, Bavaria, DE-93053, Germany
| | - Diana Ikasalaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Julia Wildenauer
- Biochemistry III, University of Regensburg, Regensburg, Bavaria, DE-93053, Germany
| | - Visvaldas Kairys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Laura Manelytė
- Biochemistry III, University of Regensburg, Regensburg, Bavaria, DE-93053, Germany
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4
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Regulatory roles of nucleolus organizer region-derived long non-coding RNAs. Mamm Genome 2021; 33:402-411. [PMID: 34436664 DOI: 10.1007/s00335-021-09906-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
The nucleolus is the largest sub-nuclear domain, serving primarily as the place for ribosome biogenesis. A delicately regulated function of the nucleolus is vital to the cell not only for maintaining proper protein synthesis but is also tightly associated with responses to different types of cellular stresses. Recently, several long non-coding RNAs (lncRNAs) were found to be part of the regulatory network that modulate nucleolar functions. Several of these lncRNAs are encoded in the ribosomal DNA (rDNA) repeats or are transcribed from the genomic regions that are located near the nucleolus organizer regions (NORs). In this review, we first discuss the current understanding of the sequence of the NORs and variations between different NORs. We then focus on the NOR-derived lncRNAs in mammalian cells and their functions in rRNA transcription and the organization of nucleolar structure under different cellular conditions. The identification of these lncRNAs reveals great potential of the NORs in harboring novel genes involved in the regulation of nucleolar functions.
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5
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Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription. Genes (Basel) 2021; 12:genes12070961. [PMID: 34202617 PMCID: PMC8303148 DOI: 10.3390/genes12070961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 12/29/2022] Open
Abstract
Ribosomal transcription constitutes the major energy consuming process in cells and is regulated in response to proliferation, differentiation and metabolic conditions by several signalling pathways. These act on the transcription machinery but also on chromatin factors and ncRNA. The many ribosomal gene repeats are organised in a number of different chromatin states; active, poised, pseudosilent and repressed gene repeats. Some of these chromatin states are unique to the 47rRNA gene repeat and do not occur at other locations in the genome, such as the active state organised with the HMG protein UBF whereas other chromatin state are nucleosomal, harbouring both active and inactive histone marks. The number of repeats in a certain state varies on developmental stage and cell type; embryonic cells have more rRNA gene repeats organised in an open chromatin state, which is replaced by heterochromatin during differentiation, establishing different states depending on cell type. The 47S rRNA gene transcription is regulated in different ways depending on stimulus and chromatin state of individual gene repeats. This review will discuss the present knowledge about factors involved, such as chromatin remodelling factors NuRD, NoRC, CSB, B-WICH, histone modifying enzymes and histone chaperones, in altering gene expression and switching chromatin states in proliferation, differentiation, metabolic changes and stress responses.
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6
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Oberbeckmann E, Niebauer V, Watanabe S, Farnung L, Moldt M, Schmid A, Cramer P, Peterson CL, Eustermann S, Hopfner KP, Korber P. Ruler elements in chromatin remodelers set nucleosome array spacing and phasing. Nat Commun 2021; 12:3232. [PMID: 34050140 PMCID: PMC8163753 DOI: 10.1038/s41467-021-23015-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 03/13/2021] [Indexed: 01/09/2023] Open
Abstract
Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the 'ruler' that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.
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Affiliation(s)
- Elisa Oberbeckmann
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vanessa Niebauer
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shinya Watanabe
- Program of Molecular Medicine, University of Massachusetts, Worcester, MA, USA
| | - Lucas Farnung
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Manuela Moldt
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea Schmid
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts, Worcester, MA, USA
| | - Sebastian Eustermann
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Philipp Korber
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany.
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7
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Gallenga CE, Lonardi M, Pacetti S, Violanti SS, Tassinari P, Di Virgilio F, Tognon M, Perri P. Molecular Mechanisms Related to Oxidative Stress in Retinitis Pigmentosa. Antioxidants (Basel) 2021; 10:antiox10060848. [PMID: 34073310 PMCID: PMC8229325 DOI: 10.3390/antiox10060848] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/17/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited retinopathy. Nevertheless, non-genetic biological factors play a central role in its pathogenesis and progression, including inflammation, autophagy and oxidative stress. The retina is particularly affected by oxidative stress due to its high metabolic rate and oxygen consumption as well as photosensitizer molecules inside the photoreceptors being constantly subjected to light/oxidative stress, which induces accumulation of ROS in RPE, caused by damaged photoreceptor’s daily recycling. Oxidative DNA damage is a key regulator of microglial activation and photoreceptor degeneration in RP, as well as mutations in endogenous antioxidant pathways involved in DNA repair, oxidative stress protection and activation of antioxidant enzymes (MUTYH, CERKL and GLO1 genes, respectively). Moreover, exposure to oxidative stress alters the expression of micro-RNA (miRNAs) and of long non-codingRNA (lncRNAs), which might be implicated in RP etiopathogenesis and progression, modifying gene expression and cellular response to oxidative stress. The upregulation of the P2X7 receptor (P2X7R) also seems to be involved, causing pro-inflammatory cytokines and ROS release by macrophages and microglia, contributing to neuroinflammatory and neurodegenerative progression in RP. The multiple pathways analysed demonstrate that oxidative microglial activation may trigger the vicious cycle of non-resolved neuroinflammation and degeneration, suggesting that microglia may be a key therapy target of oxidative stress in RP.
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Affiliation(s)
- Carla Enrica Gallenga
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (C.E.G.); (F.D.V.); (M.T.)
| | - Maria Lonardi
- Department of Specialized Surgery, Section of Ophthalmology, Sant’Anna University Hospital, 44121 Ferrara, Italy; (M.L.); (S.P.); (P.T.)
| | - Sofia Pacetti
- Department of Specialized Surgery, Section of Ophthalmology, Sant’Anna University Hospital, 44121 Ferrara, Italy; (M.L.); (S.P.); (P.T.)
| | - Sara Silvia Violanti
- Department of Head and Neck, Section of Ophthalmology, San Paolo Hospital, 17100 Savona, Italy;
| | - Paolo Tassinari
- Department of Specialized Surgery, Section of Ophthalmology, Sant’Anna University Hospital, 44121 Ferrara, Italy; (M.L.); (S.P.); (P.T.)
| | - Francesco Di Virgilio
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (C.E.G.); (F.D.V.); (M.T.)
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (C.E.G.); (F.D.V.); (M.T.)
| | - Paolo Perri
- Department of Neuroscience and Rehabilitation, Section of Ophthalmology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence:
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8
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Morgan A, LeGresley S, Fischer C. Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability. Int J Mol Sci 2020; 22:ijms22010076. [PMID: 33374740 PMCID: PMC7793527 DOI: 10.3390/ijms22010076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.
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9
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Rolicka A, Guo Y, Gañez Zapater A, Tariq K, Quin J, Vintermist A, Sadeghifar F, Arsenian-Henriksson M, Östlund Farrants AK. The chromatin-remodeling complexes B-WICH and NuRD regulate ribosomal transcription in response to glucose. FASEB J 2020; 34:10818-10834. [PMID: 32598531 DOI: 10.1096/fj.202000411r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022]
Abstract
Regulation of ribosomal transcription is under tight control from environmental stimuli, and this control involves changes in the chromatin structure. The underlying mechanism of how chromatin changes in response to nutrient and energy supply in the cell is still unclear. The chromatin-remodeling complex B-WICH is involved in activating the ribosomal transcription, and we show here that knock down of the B-WICH component WSTF results in cells that do not respond to glucose. The promoter is less accessible, and RNA pol I and its transcription factors SL1/TIF-1B and RRN3/TIF-1A, as well as the proto-oncogene c-MYC and the activating deacetylase SIRT7 do not bind upon glucose stimulation. In contrast, the repressive chromatin state that forms after glucose deprivation is reversible, and RNA pol I factors are recruited. WSTF knock down results in an accumulation of the ATPase CHD4, a component of the NuRD chromatin remodeling complex, which is responsible for establishing a repressive poised state at the promoter. The TTF-1, which binds and affect the binding of the chromatin complexes, is important to control the association of activating chromatin component UBF. We suggest that B-WICH is required to allow for a shift to an active chromatin state upon environmental stimulation, by counteracting the repressive state induced by the NuRD complex.
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Affiliation(s)
- Anna Rolicka
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Antoni Gañez Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Kanwal Tariq
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Jaclyn Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Anna Vintermist
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Fatemeh Sadeghifar
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum B7, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
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10
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Donato L, Scimone C, Alibrandi S, Rinaldi C, Sidoti A, D’Angelo R. Transcriptome Analyses of lncRNAs in A2E-Stressed Retinal Epithelial Cells Unveil Advanced Links between Metabolic Impairments Related to Oxidative Stress and Retinitis Pigmentosa. Antioxidants (Basel) 2020; 9:E318. [PMID: 32326576 PMCID: PMC7222347 DOI: 10.3390/antiox9040318] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022] Open
Abstract
: Long non-coding RNAs (lncRNAs) are untranslated transcripts which regulate many biological processes. Changes in lncRNA expression pattern are well-known related to various human disorders, such as ocular diseases. Among them, retinitis pigmentosa, one of the most heterogeneous inherited disorder, is strictly related to oxidative stress. However, little is known about regulative aspects able to link oxidative stress to etiopathogenesis of retinitis. Thus, we realized a total RNA-Seq experiment, analyzing human retinal pigment epithelium cells treated by the oxidant agent N-retinylidene-N-retinylethanolamine (A2E), considering three independent experimental groups (untreated control cells, cells treated for 3 h and cells treated for 6 h). Differentially expressed lncRNAs were filtered out, explored with specific tools and databases, and finally subjected to pathway analysis. We detected 3,3'-overlapping ncRNAs, 107 antisense, 24 sense-intronic, four sense-overlapping and 227 lincRNAs very differentially expressed throughout all considered time points. Analyzed lncRNAs could be involved in several biochemical pathways related to compromised response to oxidative stress, carbohydrate and lipid metabolism impairment, melanin biosynthetic process alteration, deficiency in cellular response to amino acid starvation, unbalanced regulation of cofactor metabolic process, all leading to retinal cell death. The explored lncRNAs could play a relevant role in retinitis pigmentosa etiopathogenesis, and seem to be the ideal candidate for novel molecular markers and therapeutic strategies.
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Affiliation(s)
- Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy
- Department of Biomolecular Strategies, Genetics and Avant-Garde Therapies, I.E.ME.S.T., 90139 Palermo, Italy
| | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy
- Department of Biomolecular Strategies, Genetics and Avant-Garde Therapies, I.E.ME.S.T., 90139 Palermo, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98125 Messina, Italy
| | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy
- Department of Biomolecular Strategies, Genetics and Avant-Garde Therapies, I.E.ME.S.T., 90139 Palermo, Italy
| | - Rosalia D’Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy
- Department of Biomolecular Strategies, Genetics and Avant-Garde Therapies, I.E.ME.S.T., 90139 Palermo, Italy
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11
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Pallares RM, Thanh NTK, Su X. Quantifying the binding between proteins and open chromatin-like DNA sequences with gold nanorods. Chem Commun (Camb) 2019; 55:15041-15044. [PMID: 31696164 DOI: 10.1039/c9cc07511a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of transcription factors to DNA is one of the main mechanisms in gene regulation. While transcription factors frequently bind to unwrapped long DNA sequences known as open chromatin structures, most bioassays that study protein-DNA binding rely on short oligonucleotide probes. In this work, we develop a gold nanorod-based colorimetric assay for the binding of transcription factors to DNA in long open chromatin-like structures. After the determination of the binding affinity and stoichiometry, we explored the effect of the probe length on the assay performance and compared it to other established techniques.
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Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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12
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Sawyer IA, Bartek J, Dundr M. Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing. Semin Cell Dev Biol 2018; 90:94-103. [PMID: 30017905 DOI: 10.1016/j.semcdb.2018.07.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/03/2018] [Indexed: 01/01/2023]
Abstract
Proteins and RNAs inside the cell nucleus are organized into distinct phases, also known as liquid-liquid phase separated (LLPS) droplet organelles or nuclear bodies. These regions exist within the spaces between chromatin-rich regions but their function is tightly linked to gene activity. They include major microscopically-observable structures such as the nucleolus, paraspeckle and Cajal body. The biochemical and assembly factors enriched inside these microenvironments regulate chromatin structure, transcription, and RNA processing, and other important cellular functions. Here, we describe published evidence that suggests nuclear bodies are bona fide LLPS droplet organelles and major regulators of the processes listed above. We also outline an updated "Supply or Sequester" model to describe nuclear body function, in which proteins or RNAs are supplied to surrounding genomic regions or sequestered away from their sites of activity. Finally, we describe recent evidence that suggests these microenvironments are both reflective and drivers of diverse pathophysiological states.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, United States; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jiri Bartek
- Danish Cancer, Society Research Center, Genome Integrity Unit, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, United States.
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13
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Pfab A, Grønlund JT, Holzinger P, Längst G, Grasser KD. The Arabidopsis Histone Chaperone FACT: Role of the HMG-Box Domain of SSRP1. J Mol Biol 2018; 430:2747-2759. [PMID: 29966609 DOI: 10.1016/j.jmb.2018.06.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 11/15/2022]
Abstract
Histone chaperones play critical roles in regulated structural transitions of chromatin in eukaryotic cells that involve nucleosome disassembly and reassembly. The histone chaperone FACT is a heterodimeric complex consisting in plants and metazoa of SSRP1/SPT16 and is involved in dynamic nucleosome reorganization during various DNA-dependent processes including transcription, replication and repair. The C-terminal HMG-box domain of the SSRP1 subunit mediates interactions with DNA and nucleosomes in vitro, but its relevance in vivo is unclear. Here, we demonstrate that Arabidopsis ssrp1-2 mutant plants express a C-terminally truncated SSRP1 protein. Although the structure of the truncated HMG-box domain is distinctly disturbed, it still exhibits residual DNA-binding activity, but has lost DNA-bending activity. Since ssrp1-2 plants are phenotypically affected but viable, the HMG-box domain may be functionally non-essential. To examine this possibility, SSRP1∆HMG completely lacking the HMG-box domain was studied. SSRP1∆HMG in vitro did not bind to DNA and its interactions with nucleosomes were severely reduced. Nevertheless, the protein showed a nuclear mobility and protein interactions similar to SSRP1. Interestingly, expression of SSRP1∆HMG is almost as efficient as that of full-length SSRP1 in supporting normal growth and development of the otherwise non-viable Arabidopsis ssrp1-1 mutant. SSRP1∆HMG is structurally similar to the fungal ortholog termed Pob3 that shares clear similarity with SSRP1, but it lacks the C-terminal HMG-box. Therefore, our findings indicate that the HMG-box domain conserved among SSRP1 proteins is not critical in Arabidopsis, and thus, the functionality of SSRP1/SPT16 in plants/metazoa and Pob3/Spt16 in fungi is perhaps more similar than anticipated.
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Affiliation(s)
- Alexander Pfab
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Jesper T Grønlund
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
| | - Philipp Holzinger
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Gernot Längst
- Department of Biochemistry III, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
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14
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Sokpor G, Castro-Hernandez R, Rosenbusch J, Staiger JF, Tuoc T. ATP-Dependent Chromatin Remodeling During Cortical Neurogenesis. Front Neurosci 2018; 12:226. [PMID: 29686607 PMCID: PMC5900035 DOI: 10.3389/fnins.2018.00226] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
The generation of individual neurons (neurogenesis) during cortical development occurs in discrete steps that are subtly regulated and orchestrated to ensure normal histogenesis and function of the cortex. Notably, various gene expression programs are known to critically drive many facets of neurogenesis with a high level of specificity during brain development. Typically, precise regulation of gene expression patterns ensures that key events like proliferation and differentiation of neural progenitors, specification of neuronal subtypes, as well as migration and maturation of neurons in the developing cortex occur properly. ATP-dependent chromatin remodeling complexes regulate gene expression through utilization of energy from ATP hydrolysis to reorganize chromatin structure. These chromatin remodeling complexes are characteristically multimeric, with some capable of adopting functionally distinct conformations via subunit reconstitution to perform specific roles in major aspects of cortical neurogenesis. In this review, we highlight the functions of such chromatin remodelers during cortical development. We also bring together various proposed mechanisms by which ATP-dependent chromatin remodelers function individually or in concert, to specifically modulate vital steps in cortical neurogenesis.
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Affiliation(s)
- Godwin Sokpor
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Ricardo Castro-Hernandez
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Joachim Rosenbusch
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Tran Tuoc
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
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15
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Abstract
Ribosome biogenesis is a complex and highly energy-demanding process that requires the concerted action of all three nuclear RNA polymerases (Pol I-III) in eukaryotes. The three largest ribosomal RNAs (rRNAs) originate from a precursor transcript (pre-rRNA) that is encoded by multicopy genes located in the nucleolus. Transcription of these rRNA genes (rDNA) by Pol I is the key regulation step in ribosome production and is tightly controlled by an intricate network of signaling pathways and epigenetic mechanisms. In this article, we give an overview of the composition of the basal Pol I machinery and rDNA chromatin. We discuss rRNA gene regulation in response to environmental signals and developmental cues and focus on perturbations occurring in diseases linked to either excessive or limited rRNA levels. Finally, we discuss the emerging view that rDNA integrity and activity may be involved in the aging process.
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Affiliation(s)
- Samim Sharifi
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University, 07745 Jena, Germany; , .,Leibniz-Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Holger Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University, 07745 Jena, Germany; , .,Leibniz-Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
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16
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Morgan AM, LeGresley SE, Briggs K, Al-Ani G, Fischer CJ. Effects of nucleosome stability on remodeler-catalyzed repositioning. Phys Rev E 2018; 97:032422. [PMID: 29776169 DOI: 10.1103/physreve.97.032422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 06/08/2023]
Abstract
Chromatin remodelers are molecular motors that play essential roles in the regulation of nucleosome positioning and chromatin accessibility. These machines couple the energy obtained from the binding and hydrolysis of ATP to the mechanical work of manipulating chromatin structure through processes that are not completely understood. Here we present a quantitative analysis of nucleosome repositioning by the imitation switch (ISWI) chromatin remodeler and demonstrate that nucleosome stability significantly impacts the observed activity. We show how DNA damage induced changes in the affinity of DNA wrapping within the nucleosome can affect ISWI repositioning activity and demonstrate how assay-dependent limitations can bias studies of nucleosome repositioning. Together, these results also suggest that some of the diversity seen in chromatin remodeler activity can be attributed to the variations in the thermodynamics of interactions between the remodeler, the histones, and the DNA, rather than reflect inherent properties of the remodeler itself.
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Affiliation(s)
- Aaron M Morgan
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Sarah E LeGresley
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Koan Briggs
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Gada Al-Ani
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Christopher J Fischer
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
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17
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Sawyer IA, Dundr M. Chromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture. Chromosoma 2017; 126:541-557. [PMID: 28593374 DOI: 10.1007/s00412-017-0632-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 01/18/2023]
Abstract
An intrinsic and essential trait exhibited by cells is the properly coordinated and integrated regulation of an astoundingly large number of simultaneous molecular decisions and reactions to maintain biochemical homeostasis. This is especially true inside the cell nucleus, where the recognition of DNA and RNA by a vast range of nucleic acid-interacting proteins organizes gene expression patterns. However, this dynamic system is not regulated by simple "on" or "off" signals. Instead, transcription factor and RNA polymerase recruitment to DNA are influenced by the local chromatin and epigenetic environment, a gene's relative position within the nucleus and the action of noncoding RNAs. In addition, major phase-separated structural features of the nucleus, such as nucleoli and paraspeckles, assemble in direct response to specific transcriptional activities and, in turn, influence global genomic function. Currently, the interpretation of these data is trapped in a causality dilemma reminiscent of the "chicken and the egg" paradox as it is unclear whether changes in nuclear architecture promote RNA function or vice versa. Here, we review recent advances that suggest a complex and interdependent interaction network between gene expression, chromatin topology, and noncoding RNA function. We also discuss the functional links between these essential nuclear processes from the nanoscale (gene looping) to the macroscale (sub-nuclear gene positioning and nuclear body function) and briefly highlight some of the challenges that researchers may encounter when studying these phenomena.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA.
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18
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Brázda V, Coufal J. Recognition of Local DNA Structures by p53 Protein. Int J Mol Sci 2017; 18:ijms18020375. [PMID: 28208646 PMCID: PMC5343910 DOI: 10.3390/ijms18020375] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/03/2017] [Indexed: 02/06/2023] Open
Abstract
p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
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19
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Gentry M, Hennig L. A Structural Bisulfite Assay to Identify DNA Cruciforms. MOLECULAR PLANT 2016; 9:1328-1336. [PMID: 27375204 DOI: 10.1016/j.molp.2016.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 06/10/2016] [Accepted: 06/12/2016] [Indexed: 06/06/2023]
Abstract
In the half century since the discovery of the double-helix structure of DNA, it has become increasingly clear that DNA functionality is based on much more than its sequence in a double-helical structure. Further advances have highlighted the importance of additional aspects of DNA structure: its packaging in the higher order chromatin structure, positioning of nucleosomes along the DNA, and the occurrence of non-helical DNA structures. Of these, the latter has been problematic to prove empirically. Here, we describe a method that uses non-denaturing bisulfite sequencing on isolated Arabidopsis thaliana nuclei to determine the location of cytosines positioned outside the double helix as a result of non-B-form DNA structures. We couple this with computational methods and S1 nuclease digest to reliably identify stable, non-B-form, cruciform structures. This enables us to identify a palindrome in the promoter of FLOWERING LOCUS T that forms a stable non-B-form structure. The stronger conservation of the ability to form a non-helical secondary structure than of the sequence suggests that this structure is biologically relevant.
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Affiliation(s)
- Matthew Gentry
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden.
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20
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Signal B, Gloss BS, Dinger ME. Computational Approaches for Functional Prediction and Characterisation of Long Noncoding RNAs. Trends Genet 2016; 32:620-637. [PMID: 27592414 DOI: 10.1016/j.tig.2016.08.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 02/09/2023]
Abstract
Although a considerable portion of eukaryotic genomes is transcribed as long noncoding RNAs (lncRNAs), the vast majority are functionally uncharacterised. The rapidly expanding catalogue of mechanistically investigated lncRNAs has provided evidence for distinct functional subclasses, which are now ripe for exploitation as a general model to predict functions for uncharacterised lncRNAs. By utilising publicly-available genome-wide datasets and computational methods, we present several developed and emerging in silico approaches to characterise and predict the functions of lncRNAs. We propose that the application of these techniques provides valuable functional and mechanistic insight into lncRNAs, and is a crucial step for informing subsequent functional studies.
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Affiliation(s)
- Bethany Signal
- Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Brian S Gloss
- Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, Australia.
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21
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Liu H, Wang P, Liu L, Min Z, Luo K, Wan Y. Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae. Sci Rep 2015; 5:15583. [PMID: 26498326 PMCID: PMC4620441 DOI: 10.1038/srep15583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/28/2015] [Indexed: 01/13/2023] Open
Abstract
Nucleosome organization exhibits dynamic properties depending on the cell state and environment. Histone proteins, fundamental components of nucleosomes, are subject to chemical modifications on particular residues. We examined the effect of substituting modifiable residues of four core histones with the non-modifiable residue alanine on nucleosome dynamics. We mapped the genome-wide nucleosomes in 22 histone mutants of Saccharomyces cerevisiae and compared the nucleosome alterations relative to the wild-type strain. Our results indicated that different types of histone mutation resulted in different phenotypes and a distinct reorganization of nucleosomes. Nucleosome occupancy was altered at telomeres, but not at centromeres. The first nucleosomes upstream (−1) and downstream (+1) of the transcription start site (TSS) were more dynamic than other nucleosomes. Mutations in histones affected the nucleosome array downstream of the TSS. Highly expressed genes, such as ribosome genes and genes involved in glycolysis, showed increased nucleosome occupancy in many types of histone mutant. In particular, the H3K56A mutant exhibited a high percentage of dynamic genomic regions, decreased nucleosome occupancy at telomeres, increased occupancy at the +1 and −1 nucleosomes, and a slow growth phenotype under stress conditions. Our findings provide insight into the influence of histone mutations on nucleosome dynamics.
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Affiliation(s)
- Hongde Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Pingyan Wang
- Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Lingjie Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Zhu Min
- Institute of Life Sciences, Southeast University, Nanjing 210096, China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kun Luo
- Department of Neurosurgery, Xinjiang Evidence-Based Medicine Research Institute, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Yakun Wan
- Institute of Life Sciences, Southeast University, Nanjing 210096, China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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22
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Stanne T, Narayanan MS, Ridewood S, Ling A, Witmer K, Kushwaha M, Wiesler S, Wickstead B, Wood J, Rudenko G. Identification of the ISWI Chromatin Remodeling Complex of the Early Branching Eukaryote Trypanosoma brucei. J Biol Chem 2015; 290:26954-26967. [PMID: 26378228 PMCID: PMC4646403 DOI: 10.1074/jbc.m115.679019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 12/25/2022] Open
Abstract
ISWI chromatin remodelers are highly conserved in eukaryotes and are important for the assembly and spacing of nucleosomes, thereby controlling transcription initiation and elongation. ISWI is typically associated with different subunits, forming specialized complexes with discrete functions. In the unicellular parasite Trypanosoma brucei, which causes African sleeping sickness, TbISWI down-regulates RNA polymerase I (Pol I)-transcribed variant surface glycoprotein (VSG) gene expression sites (ESs), which are monoallelically expressed. Here, we use tandem affinity purification to determine the interacting partners of TbISWI. We identify three proteins that do not show significant homology with known ISWI-associated partners. Surprisingly, one of these is nucleoplasmin-like protein (NLP), which we had previously shown to play a role in ES control. In addition, we identify two novel ISWI partners, regulator of chromosome condensation 1-like protein (RCCP) and phenylalanine/tyrosine-rich protein (FYRP), both containing protein motifs typically found on chromatin proteins. Knockdown of RCCP or FYRP in bloodstream form T. brucei results in derepression of silent variant surface glycoprotein ESs, as had previously been shown for TbISWI and NLP. All four proteins are expressed and interact with each other in both major life cycle stages and show similar distributions at Pol I-transcribed loci. They are also found at Pol II strand switch regions as determined with ChIP. ISWI, NLP, RCCP, and FYRP therefore appear to form a single major ISWI complex in T. brucei (TbIC). This reduced complexity of ISWI regulation and the presence of novel ISWI partners highlights the early divergence of trypanosomes in evolution.
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Affiliation(s)
- Tara Stanne
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Mani Shankar Narayanan
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Sophie Ridewood
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Alexandra Ling
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Kathrin Witmer
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Manish Kushwaha
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Simone Wiesler
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Bill Wickstead
- the School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Jennifer Wood
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Gloria Rudenko
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and.
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23
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Chromatin Remodelers: From Function to Dysfunction. Genes (Basel) 2015; 6:299-324. [PMID: 26075616 PMCID: PMC4488666 DOI: 10.3390/genes6020299] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 12/20/2022] Open
Abstract
Chromatin remodelers are key players in the regulation of chromatin accessibility and nucleosome positioning on the eukaryotic DNA, thereby essential for all DNA dependent biological processes. Thus, it is not surprising that upon of deregulation of those molecular machines healthy cells can turn into cancerous cells. Even though the remodeling enzymes are very abundant and a multitude of different enzymes and chromatin remodeling complexes exist in the cell, the particular remodeling complex with its specific nucleosome positioning features must be at the right place at the right time in order to ensure the proper regulation of the DNA dependent processes. To achieve this, chromatin remodeling complexes harbor protein domains that specifically read chromatin targeting signals, such as histone modifications, DNA sequence/structure, non-coding RNAs, histone variants or DNA bound interacting proteins. Recent studies reveal the interaction between non-coding RNAs and chromatin remodeling complexes showing importance of RNA in remodeling enzyme targeting, scaffolding and regulation. In this review, we summarize current understanding of chromatin remodeling enzyme targeting to chromatin and their role in cancer development.
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24
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Spt6 Is Essential for rRNA Synthesis by RNA Polymerase I. Mol Cell Biol 2015; 35:2321-31. [PMID: 25918242 DOI: 10.1128/mcb.01499-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/19/2015] [Indexed: 01/04/2023] Open
Abstract
Spt6 (suppressor of Ty6) has many roles in transcription initiation and elongation by RNA polymerase (Pol) II. These effects are mediated through interactions with histones, transcription factors, and the RNA polymerase. Two lines of evidence suggest that Spt6 also plays a role in rRNA synthesis. First, Spt6 physically associates with a Pol I subunit (Rpa43). Second, Spt6 interacts physically and genetically with Spt4/5, which directly affects Pol I transcription. Utilizing a temperature-sensitive allele, spt6-1004, we show that Spt6 is essential for Pol I occupancy of the ribosomal DNA (rDNA) and rRNA synthesis. Our data demonstrate that protein levels of an essential Pol I initiation factor, Rrn3, are reduced when Spt6 is inactivated, leading to low levels of Pol I-Rrn3 complex. Overexpression of RRN3 rescues Pol I-Rrn3 complex formation; however, rRNA synthesis is not restored. These data suggest that Spt6 is involved in either recruiting the Pol I-Rrn3 complex to the rDNA or stabilizing the preinitiation complex. The findings presented here identify an unexpected, essential role for Spt6 in synthesis of rRNA.
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25
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Lafontaine DLJ. Noncoding RNAs in eukaryotic ribosome biogenesis and function. Nat Struct Mol Biol 2015; 22:11-9. [PMID: 25565028 DOI: 10.1038/nsmb.2939] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
The ribosome, central to protein synthesis in all cells, is a complex multicomponent assembly with rRNA at its functional core. During the process of ribosome biogenesis, diverse noncoding RNAs participate in controlling the quantity and quality of this rRNA. In this Review, I discuss the multiple roles assumed by noncoding RNAs during the different steps of ribosome biogenesis and how they contribute to the generation of ribosome heterogeneity, which affects normal and pathophysiological processes.
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Affiliation(s)
- Denis L J Lafontaine
- RNA Molecular Biology, Fonds National de la Recherche Scientifique, Université Libre de Bruxelles, Brussels, Belgium
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