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Ferrari KJ, Amato S, Noberini R, Toscani C, Fernández-Pérez D, Rossi A, Conforti P, Zanotti M, Bonaldi T, Tamburri S, Pasini D. Intestinal differentiation involves cleavage of histone H3 N-terminal tails by multiple proteases. Nucleic Acids Res 2021; 49:791-804. [PMID: 33398338 PMCID: PMC7826276 DOI: 10.1093/nar/gkaa1228] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/14/2022] Open
Abstract
The proteolytic cleavage of histone tails, also termed histone clipping, has been described as a mechanism for permanent removal of post-translational modifications (PTMs) from histone proteins. Such activity has been ascribed to ensure regulatory function in key cellular processes such as differentiation, senescence and transcriptional control, for which different histone-specific proteases have been described. However, all these studies were exclusively performed using cell lines cultured in vitro and no clear evidence that histone clipping is regulated in vivo has been reported. Here we show that histone H3 N-terminal tails undergo extensive cleavage in the differentiated cells of the villi in mouse intestinal epithelium. Combining biochemical methods, 3D organoid cultures and in vivo approaches, we demonstrate that intestinal H3 clipping is the result of multiple proteolytic activities. We identified Trypsins and Cathepsin L as specific H3 tail proteases active in small intestinal differentiated cells and showed that their proteolytic activity is differentially affected by the PTM pattern of histone H3 tails. Together, our findings provide in vivo evidence of H3 tail proteolysis in mammalian tissues, directly linking H3 clipping to cell differentiation.
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Affiliation(s)
- Karin Johanna Ferrari
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Amato
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Roberta Noberini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Cecilia Toscani
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Daniel Fernández-Pérez
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Alessandra Rossi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Pasquale Conforti
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marika Zanotti
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simone Tamburri
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Diego Pasini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
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Tabatabaiefar MA, Sajjadi RS, Narrei S. Epigenetics and Common Non Communicable Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1121:7-20. [PMID: 31392648 DOI: 10.1007/978-3-030-10616-4_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Common Non communicable diseases (NCDs), such as cardiovascular disease, cancer, schizophrenia, and diabetes, have become the major cause of death in the world. They result from an interaction between genetics, lifestyle and environmental factors. The prevalence of NCDs are increasing, and researchers hopes to find efficient strategies to predict, prevent and treat them. Given the role of epigenome in the etiology of NCDs, insight into epigenetic mechanisms may offer opportunities to predict, detect, and prevent disease long before its clinical onset.Epigenetic alterations are exerted through several mechanisms including: chromatin modification, DNA methylation and controlling gene expression by non-coding RNAs (ncRNAs). In this chapter, we will discuss about NCDs, with focus on cancer, diabetes and schizophrenia. Different epigenetic mechanisms, categorized into two main groups DNA methylation and chromatin modifications and non-coding RNAs, will be separately discussed for these NCDs.
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Affiliation(s)
- Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran. .,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran. .,Genetics Department, Erythron Pathobiology and Genetics lab, Isfahan, Iran.
| | - Roshanak S Sajjadi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sina Narrei
- Genetics Department, Erythron Pathobiology and Genetics lab, Isfahan, Iran
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Azad GK, Swagatika S, Kumawat M, Kumawat R, Tomar RS. Modifying Chromatin by Histone Tail Clipping. J Mol Biol 2018; 430:3051-3067. [DOI: 10.1016/j.jmb.2018.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/15/2022]
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Brunet FG, Audit B, Drillon G, Argoul F, Volff JN, Arneodo A. Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates. Biophys J 2018; 114:2308-2316. [PMID: 29580552 PMCID: PMC6028776 DOI: 10.1016/j.bpj.2018.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/07/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022] Open
Abstract
Nucleosome-depleted regions around which nucleosomes order following the "statistical" positioning scenario were recently shown to be encoded in the DNA sequence in human. This intrinsic nucleosomal ordering strongly correlates with oscillations in the local GC content as well as with the interspecies and intraspecies mutation profiles, revealing the existence of both positive and negative selection. In this letter, we show that these predicted nucleosome inhibitory energy barriers (NIEBs) with compacted neighboring nucleosomes are indeed ubiquitous to all vertebrates tested. These 1 kb-sized chromatin patterns are widely distributed along vertebrate chromosomes, overall covering more than a third of the genome. We have previously observed in human deviations from neutral evolution at these genome-wide distributed regions, which we interpreted as a possible indication of the selection of an open, accessible, and dynamic nucleosomal array to constitutively facilitate the epigenetic regulation of nuclear functions in a cell-type-specific manner. As a first, very appealing observation supporting this hypothesis, we report evidence of a strong association between NIEB borders and the poly(A) tails of Alu sequences in human. These results suggest that NIEBs provide adequate chromatin patterns favorable to the integration of Alu retrotransposons and, more generally to various transposable elements in the genomes of primates and other vertebrates.
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Affiliation(s)
- Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, Lyon, France
| | - Benjamin Audit
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France
| | - Guénola Drillon
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France
| | - Françoise Argoul
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France; LOMA, Université de Bordeaux, CNRS UMR 5798, Talence, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, Lyon, France
| | - Alain Arneodo
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France; LOMA, Université de Bordeaux, CNRS UMR 5798, Talence, France.
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5
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Drillon G, Audit B, Argoul F, Arneodo A. Evidence of selection for an accessible nucleosomal array in human. BMC Genomics 2016; 17:526. [PMID: 27472913 PMCID: PMC4966569 DOI: 10.1186/s12864-016-2880-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/04/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Recently, a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix has been used to reveal some enrichment of nucleosome-inhibiting energy barriers (NIEBs) nearby ubiquitous human "master" replication origins. Here we use this model to predict the existence of about 1.6 millions NIEBs over the 22 human autosomes. RESULTS We show that these high energy barriers of mean size 153 bp correspond to nucleosome-depleted regions (NDRs) in vitro, as expected, but also in vivo. On either side of these NIEBs, we observe, in vivo and in vitro, a similar compacted nucleosome ordering, suggesting an absence of chromatin remodeling. This nucleosomal ordering strongly correlates with oscillations of the GC content as well as with the interspecies and intraspecies mutation profiles along these regions. Comparison of these divergence rates reveals the existence of both positive and negative selections linked to nucleosome positioning around these intrinsic NDRs. Overall, these NIEBs and neighboring nucleosomes cover 37.5 % of the human genome where nucleosome occupancy is stably encoded in the DNA sequence. These 1 kb-sized regions of intrinsic nucleosome positioning are equally found in GC-rich and GC-poor isochores, in early and late replicating regions, in intergenic and genic regions but not at gene promoters. CONCLUSION The source of selection pressure on the NIEBs has yet to be resolved in future work. One possible scenario is that these widely distributed chromatin patterns have been selected in human to impair the condensation of the nucleosomal array into the 30 nm chromatin fiber, so as to facilitate the epigenetic regulation of nuclear functions in a cell-type-specific manner.
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Affiliation(s)
- Guénola Drillon
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
| | - Benjamin Audit
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
| | - Françoise Argoul
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
- LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, F-33405 France
| | - Alain Arneodo
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
- LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, F-33405 France
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Simon N, Ebert C, Schneider S. Structural Basis for Bulky-Adduct DNA-Lesion Recognition by the Nucleotide Excision Repair Protein Rad14. Chemistry 2016; 22:10782-5. [DOI: 10.1002/chem.201602438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Nina Simon
- Center for Integrated Protein Science Munich CIPSM; Department of Chemistry; Ludwig-Maximilians Universität München; Butenandtstrasse 13 81377 München Germany
| | - Charlotte Ebert
- Center for Integrated Protein Science Munich CIPSM; Department of Chemistry; Ludwig-Maximilians Universität München; Butenandtstrasse 13 81377 München Germany
| | - Sabine Schneider
- Center for Integrated Protein Science Munich CIPSM; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
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7
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Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
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Trifonov EN, Tripathi V. Strong nucleosomes of yeasts. J Biomol Struct Dyn 2015; 34:439-47. [PMID: 25893982 DOI: 10.1080/07391102.2015.1026940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Yeast genome lacks visibly periodic sequences characteristic of strong nucleosomes (SNs) originally discovered in A. thaliana, C. elegans, and H. sapiens. Yet, the sequences with good match to the (RRRRRYYYYY)n consensus of the SNs do show preference to centromere regions of Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Cryptococcus neoformans - property characteristic of SNs of higher eukaryotes. Candida albicans is the first exception detected so far, where their SNs do not have any affinity to the centromeres, nor pericentromeric regions. Three of the four yeast genomes analyzed possess unique repeating centromere-specific SN sequences (C. albicans, again, is an exception). The results firmly indicate that centromeres of plants, animals, and yeasts in general have special chromatin structure, favoring SNs.
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Affiliation(s)
- Edward N Trifonov
- a Genome Diversity Center, Institute of Evolution , University of Haifa , Mount Carmel, Haifa 3498838 , Israel
| | - Vijay Tripathi
- a Genome Diversity Center, Institute of Evolution , University of Haifa , Mount Carmel, Haifa 3498838 , Israel
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Oh J, Sanders IF, Chen EZ, Li H, Tobias JW, Isett RB, Penubarthi S, Sun H, Baldwin DA, Fraser NW. Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection. PLoS One 2015; 10:e0117471. [PMID: 25710170 PMCID: PMC4339549 DOI: 10.1371/journal.pone.0117471] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 12/23/2014] [Indexed: 01/01/2023] Open
Abstract
HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis. Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes). During lytic infection, partial micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA. However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the lytic infection, but that they are not evenly positioned, with a 200 bp repeat pattern, like cell DNA. Where then are the nucleosomes positioned? Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is in full swing (6 hr PI), using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152 kb). Arrays were probed with MNase-protected fragments of DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes. The data show that nucleosome deposition is not random. The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (nucleosome free regions -NFR or Nucleosome depleted regions -NDR), or occupied at frequency below our limit of detection in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during lytic infection. On average, DNA encoding Immediate Early (IE), Early (E) and Late (L) genes appear to have a similar density of nucleosomes.
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Affiliation(s)
- Jaewook Oh
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Iryna F. Sanders
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Eric Z. Chen
- Department of Chemical Pathology, The Chinese University of Hong Kong, Li Ka Shing Institute of Health Sciences, Hong Kong SAR, China
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - John W. Tobias
- Penn Molecular Profiling Facility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - R. Benjamin Isett
- Penn Molecular Profiling Facility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Sindura Penubarthi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Hao Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Li Ka Shing Institute of Health Sciences, Hong Kong SAR, China
| | - Don A. Baldwin
- Pathonomics LLC, Philadelphia, PA, 19104, United States of America
| | - Nigel W. Fraser
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
- * E-mail:
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Drillon G, Audit B, Argoul F, Arneodo A. Ubiquitous human 'master' origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064102. [PMID: 25563930 DOI: 10.1088/0953-8984/27/6/064102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
As the elementary building block of eukaryotic chromatin, the nucleosome is at the heart of the compromise between the necessity of compacting DNA in the cell nucleus and the required accessibility to regulatory proteins. The recent availability of genome-wide experimental maps of nucleosome positions for many different organisms and cell types has provided an unprecedented opportunity to elucidate to what extent the DNA sequence conditions the primary structure of chromatin and in turn participates in the chromatin-mediated regulation of nuclear functions, such as gene expression and DNA replication. In this study, we use in vivo and in vitro genome-wide nucleosome occupancy data together with the set of nucleosome-free regions (NFRs) predicted by a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix, to investigate the role of intrinsic nucleosome occupancy in the regulation of the replication spatio-temporal programme in human. We focus our analysis on the so-called replication U/N-domains that were shown to cover about half of the human genome in the germline (skew-N domains) as well as in embryonic stem cells, somatic and HeLa cells (mean replication timing U-domains). The 'master' origins of replication (MaOris) that border these megabase-sized U/N-domains were found to be specified by a few hundred kb wide regions that are hyper-sensitive to DNase I cleavage, hypomethylated, and enriched in epigenetic marks involved in transcription regulation, the hallmarks of localized open chromatin structures. Here we show that replication U/N-domain borders that are conserved in all considered cell lines have an environment highly enriched in nucleosome-excluding-energy barriers, suggesting that these ubiquitous MaOris have been selected during evolution. In contrast, MaOris that are cell-type-specific are mainly regulated epigenetically and are no longer favoured by a local abundance of intrinsic NFRs encoded in the DNA sequence. At the smaller few hundred bp scale of gene promoters, CpG-rich promoters of housekeeping genes found nearby ubiquitous MaOris as well as CpG-poor promoters of tissue-specific genes found nearby cell-type-specific MaOris, both correspond to in vivo NFRs that are not coded as nucleosome-excluding-energy barriers. Whereas the former promoters are likely to correspond to high occupancy transcription factor binding regions, the latter are an illustration that gene regulation in human is typically cell-type-specific.
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Affiliation(s)
- Guénola Drillon
- Université de Lyon, F-69000 Lyon, France. Laboratoire de Physique, CNRS UMR 5672, École Normale Supérieure de Lyon, F-69007 Lyon, France
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11
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Abstract
Nucleosome is a histone-DNA complex known as the fundamental repeating unit of chromatin. Up to 90% of eukaryotic DNA is wrapped around consecutive octamers made of the core histones H2A, H2B, H3 and H4. Nucleosome positioning affects numerous cellular processes that require robust and timely access to genomic DNA, which is packaged into the tight confines of the cell nucleus. In living cells, nucleosome positions are determined by intrinsic histone-DNA sequence preferences, competition between histones and other DNA-binding proteins for genomic sequence, and ATP-dependent chromatin remodelers. We discuss the major energetic contributions to nucleosome formation and remodeling, focusing especially on partial DNA unwrapping off the histone octamer surface. DNA unwrapping enables efficient access to nucleosome-buried binding sites and mediates rapid nucleosome removal through concerted action of two or more DNA-binding factors. High-resolution, genome-scale maps of distances between neighboring nucleosomes have shown that DNA unwrapping and nucleosome crowding (mutual invasion of nucleosome territories) are much more common than previously thought. Ultimately, constraints imposed by nucleosome energetics on the rates of ATP-dependent and spontaneous chromatin remodeling determine nucleosome occupancy genome-wide, and shape pathways of cellular response to environmental stresses.
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12
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Abstract
Recently developed latest version of the sequence-directed single-base resolution nucleosome mapping reveals existence of strong nucleosomes and chromatin columnar structures (columns). Broad application of this simple technique for further studies of chromatin and chromosome structure requires some basic understanding as to how it works and what information it affords. The paper provides such an introduction to the method. The oscillating maps of singular nucleosomes, of short and long oligonucleosome columns, are explained, as well as maps of chromatin on satellite DNA and occurrences of counter-phase (antiparallel) nucleosome neighbors.
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Affiliation(s)
- Reshma Nibhani
- a Institute of Evolution , University of Haifa , Haifa , Israel
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13
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Harteis S, Schneider S. Making the bend: DNA tertiary structure and protein-DNA interactions. Int J Mol Sci 2014; 15:12335-63. [PMID: 25026169 PMCID: PMC4139847 DOI: 10.3390/ijms150712335] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 12/11/2022] Open
Abstract
DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence ("base readout") as well as the intrinsic DNA structure ("shape recognition"). These recognition mechanisms do not exist in isolation but, depending on the individual interaction partners, are combined to various extents. Driving force for the interaction between protein and DNA remain the unique thermodynamics of each individual DNA-protein pair. In this review we focus on the structures and conformations adopted by DNA, both influenced by and influencing the specific interaction with the corresponding protein binding partner, as well as their underlying thermodynamics.
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Affiliation(s)
- Sabrina Harteis
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
| | - Sabine Schneider
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
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14
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Damaschke NA, Yang B, Bhusari S, Svaren JP, Jarrard D. Epigenetic susceptibility factors for prostate cancer with aging. Prostate 2013; 73:1721-30. [PMID: 23999928 PMCID: PMC4237278 DOI: 10.1002/pros.22716] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/06/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Increasing age is a significant risk factor for prostate cancer. The prostate is exposed to environmental and endogenous stress that may underlie this remarkable incidence. DNA methylation, genomic imprinting, and histone modifications are examples of epigenetic factors known to undergo change in the aging and cancerous prostate. In this review we examine the data linking epigenetic alterations in the prostate with aging to cancer development. METHODS An online search of current and past peer reviewed literature on epigenetic changes with cancer and aging was performed. Relevant articles were analyzed. RESULTS Epigenetic changes are responsible for modifying expression of oncogenes and tumor suppressors. Several of these changes may represent a field defect that predisposes to cancer development. Focal hypermethylation occurs at CpG islands in the promoters of certain genes including GSTP1, RARβ2, and RASSF1A with both age and cancer, while global hypomethylation is seen in prostate cancer and known to occur in the colon and other organs. A loss of genomic imprinting is responsible for biallelic expression of the well-known Insulin-like Growth Factor 2 (IGF2) gene. Loss of imprinting (LOI) at IGF2 has been documented in cancer and is also known to occur in benign aging prostate tissue marking the presence of cancer. Histone modifications have the ability to dictate chromatin structure and direct gene expression. CONCLUSIONS Epigenetic changes with aging represent molecular mechanisms to explain the increased susceptibly of the prostate to develop cancer in older men. These changes may provide an opportunity for diagnostic and chemopreventive strategies given the epigenome can be modified.
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Affiliation(s)
- N. A. Damaschke
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - B. Yang
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - S. Bhusari
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - J. P. Svaren
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, 53972
- University of Wisconsin Carbone Comprehensive Cancer Center, Madison, Wisconsin
| | - D.F. Jarrard
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
- University of Wisconsin Carbone Comprehensive Cancer Center, Madison, Wisconsin
- Environmental and Molecular Toxicology, University of Wisconsin, Madison, Wisconsin
- Correspondence to: D.F. Jarrard, MD, 7037 Wisconsin Institutes of Medical Research, 1111 Highland Avenue, Madison, WI 53792.
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15
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Muskhelishvili G, Travers A. Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell Mol Life Sci 2013; 70:4555-67. [PMID: 23771629 PMCID: PMC11113758 DOI: 10.1007/s00018-013-1394-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 11/29/2022]
Abstract
Understanding genetic regulation is a problem of fundamental importance. Recent studies have made it increasingly evident that, whereas the cellular genetic regulation system embodies multiple disparate elements engaged in numerous interactions, the central issue is the genuine function of the DNA molecule as information carrier. Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer. These two DNA information types are intrinsically coupled in the primary sequence organisation, and this coupling is directly relevant to regulation of the genetic function. In this review, we emphasise the critical need of holistic integration of the DNA information as a prerequisite for understanding the organisational complexity of the genetic regulation system.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany,
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16
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Abstract
How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.
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Abstract
PURPOSE OF REVIEW Epigenetic mechanisms have the ability to alter the phenotype without changing the genetic code. The science of epigenetics has grown considerably in recent years, and future epigenetically based treatments or prevention strategies are likely. Epigenetic associations with asthma have received growing interest because genetic and environmental factors have been unable to independently explain the cause of asthma. RECENT FINDINGS Recent findings suggest that both the environment and underlying genetic sequence variation influence DNA methylation, which in turn seems to modify the risk conferred by genetic variants for various asthma phenotypes. In particular, DNA methylation may act as an archive of a variety of early developmental exposures, which then can modify the risk related to genetic variants. SUMMARY Current asthma treatments may control the symptoms of asthma but do not modify its natural history. Epigenetic mechanisms and novel explanatory models provide burgeoning approaches to significantly increase our understanding of the initiation and progression of asthma. Due to the inheritance of epigenetics, we anticipate a rapid emergence of critical information that will provide novel treatment strategies for asthma in the current generation and ultimately the prevention of asthma in future generations.
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Julienne H, Zoufir A, Audit B, Arneodo A. Epigenetic regulation of the human genome: coherence between promoter activity and large-scale chromatin environment. FRONTIERS IN LIFE SCIENCE 2013. [DOI: 10.1080/21553769.2013.832706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Locke G, Haberman D, Johnson SM, Morozov AV. Global remodeling of nucleosome positions in C. elegans. BMC Genomics 2013; 14:284. [PMID: 23622142 PMCID: PMC3663828 DOI: 10.1186/1471-2164-14-284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 04/17/2013] [Indexed: 11/24/2022] Open
Abstract
Background Eukaryotic chromatin architecture is affected by intrinsic histone-DNA sequence preferences, steric exclusion between nucleosome particles, formation of higher-order structures, and in vivo activity of chromatin remodeling enzymes. Results To disentangle sequence-dependent nucleosome positioning from the other factors, we have created two high-throughput maps of nucleosomes assembled in vitro on genomic DNA from the nematode worm Caenorhabditis elegans. A comparison of in vitro nucleosome positions with those observed in a mixed-stage, mixed-tissue population of C. elegans cells reveals that in vivo sequence preferences are modified on the genomic scale. Indeed, G/C dinucleotides are predicted to be most favorable for nucleosome formation in vitro but not in vivo. Nucleosome sequence read coverage in vivo is distinctly lower in chromosome arms than in central regions; the observed changes in apparent nucleosome sequence specificity, likely due to genome-wide chromatin remodeler activity, contribute to the formation of these megabase-scale chromatin domains. We also observe that the majority of well-positioned in vivo nucleosomes do not occupy thermodynamically favorable sequences observed in vitro. Finally, we find that exons are intrinsically more amenable to nucleosome formation compared to introns. Nucleosome occupancy of introns and exons consistently increases with G/C content in vitro but not in vivo, in agreement with our observation that G/C dinucleotide enrichment does not strongly promote in vivo nucleosome formation. Conclusions Our findings highlight the importance of both sequence specificity and active nucleosome repositioning in creating large-scale chromatin domains, and the antagonistic roles of intrinsic sequence preferences and chromatin remodelers in C. elegans. Sequence read data has been deposited into Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra; accession number SRA050182). Additional data, software and computational predictions are available on the Nucleosome Explorer website (http://nucleosome.rutgers.edu).
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Affiliation(s)
- George Locke
- Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
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From beads on a string to the pearls of regulation: the structure and dynamics of chromatin. Biochem Soc Trans 2012; 40:331-4. [PMID: 22435807 DOI: 10.1042/bst20120011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The assembly of eukaryotic chromatin, and the bearing of its structural organization on the regulation of gene expression, were the central topics of a recent conference organized jointly by the Biochemical Society and Wellcome Trust. A range of talks and poster presentations covered topical aspects of this research field and illuminated recent advances in our understanding of the structure and function of chromatin. The two-day meeting had stimulating presentations complemented with lively discourse and interactions of participants. In the present paper, we summarize the topics presented at the meeting, in particular highlighting subjects that are reviewed in more detail within this issue of Biochemical Society Transactions. The reports bring to life the truly fascinating molecular and structural biology of chromatin.
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