1
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Lee CSK, Weiβ M, Hamperl S. Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes. Nucleus 2023; 14:2229642. [PMID: 37469113 PMCID: PMC10361152 DOI: 10.1080/19491034.2023.2229642] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive 'identity code' that defines origins based on specific nucleotide sequences, DNA structural features, the local chromatin environment, or 3D genome architecture is still missing. In this article, we review the genetic and epigenetic features of replication origins in yeast and metazoan chromosomes and highlight recent insights into how this flexibility in origin usage contributes to nuclear organization, cell growth, differentiation, and genome stability.
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Affiliation(s)
- Clare S K Lee
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Matthias Weiβ
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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2
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Amigo R, Raiqueo F, Tarifeño E, Farkas C, Gutiérrez JL. Poly(dA:dT) Tracts Differentially Modulate Nucleosome Remodeling Activity of RSC and ISW1a Complexes, Exerting Tract Orientation-Dependent and -Independent Effects. Int J Mol Sci 2023; 24:15245. [PMID: 37894925 PMCID: PMC10607297 DOI: 10.3390/ijms242015245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
The establishment and maintenance of nucleosome-free regions (NFRs) are prominent processes within chromatin dynamics. Transcription factors, ATP-dependent chromatin remodeling complexes (CRCs) and DNA sequences are the main factors involved. In Saccharomyces cerevisiae, CRCs such as RSC contribute to chromatin opening at NFRs, while other complexes, including ISW1a, contribute to NFR shrinking. Regarding DNA sequences, growing evidence points to poly(dA:dT) tracts as playing a direct role in active processes involved in nucleosome positioning dynamics. Intriguingly, poly(dA:dT)-tract-containing NFRs span asymmetrically relative to the location of the tract by a currently unknown mechanism. In order to obtain insight into the role of poly(dA:dT) tracts in nucleosome remodeling, we performed a systematic analysis of their influence on the activity of ISW1a and RSC complexes. Our results show that poly(dA:dT) tracts differentially affect the activity of these CRCs. Moreover, we found differences between the effects exerted by the two alternative tract orientations. Remarkably, tract-containing linker DNA is taken as exit DNA for nucleosome sliding catalyzed by RSC. Our findings show that defined DNA sequences, when present in linker DNA, can dictate in which direction a remodeling complex has to slide nucleosomes and shed light into the mechanisms underlying asymmetrical chromatin opening around poly(dA:dT) tracts.
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Affiliation(s)
- Roberto Amigo
- Laboratory of Transcriptional Regulation, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, Concepción 4070043, Chile; (R.A.); (F.R.); (E.T.)
| | - Fernanda Raiqueo
- Laboratory of Transcriptional Regulation, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, Concepción 4070043, Chile; (R.A.); (F.R.); (E.T.)
| | - Estefanía Tarifeño
- Laboratory of Transcriptional Regulation, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, Concepción 4070043, Chile; (R.A.); (F.R.); (E.T.)
| | - Carlos Farkas
- Biomedical Sciences Research Laboratory, Department of Basic Sciences and Morphology, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile;
| | - José L. Gutiérrez
- Laboratory of Transcriptional Regulation, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, Concepción 4070043, Chile; (R.A.); (F.R.); (E.T.)
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3
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Poulet A, Kratkiewicz AJ, Li D, van Wolfswinkel JC. Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy. SCIENCE ADVANCES 2023; 9:eadh4887. [PMID: 37801496 PMCID: PMC10558129 DOI: 10.1126/sciadv.adh4887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/05/2023] [Indexed: 10/08/2023]
Abstract
Many highly regenerative organisms maintain adult pluripotent stem cells throughout their life, but how the long-term maintenance of pluripotency is accomplished is unclear. To decipher the regulatory logic of adult pluripotent stem cells, we analyzed the chromatin organization of stem cell genes in the planarian Schmidtea mediterranea. We identify a special chromatin state of stem cell genes, which is distinct from that of tissue-specific genes and resembles constitutive genes. Where tissue-specific promoters have detectable transcription factor binding sites, the promoters of stem cell-specific genes instead have sequence features that broadly decrease nucleosome binding affinity. This genic organization makes pluripotency-related gene expression the default state in these cells, which is maintained by the activity of chromatin remodelers ISWI and SNF2 in the stem cells.
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Affiliation(s)
- Axel Poulet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Arcadia J. Kratkiewicz
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Danyan Li
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Josien C. van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Yale Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06511, USA
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4
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Abstract
Nearly three-fourths of all eukaryotic DNA is occupied by nucleosomes, protein-DNA complexes comprising octameric histone core proteins and ∼150 base pairs of DNA. In addition to acting as a DNA compaction vehicle, the dynamics of nucleosomes regulate the DNA site accessibility for the nonhistone proteins, thereby controlling regulatory processes involved in determining the cell identity and cell fate. Here, we propose an analytical framework to analyze the role of nucleosome dynamics on the target search process of transcription factors through a simple discrete-state stochastic description of the search process. By considering the experimentally determined kinetic rates associated with protein and nucleosome dynamics as the only inputs, we estimate the target search time of a protein via first-passage probability calculations separately during nucleosome breathing and sliding dynamics. Although both the nucleosome dynamics permit transient access to the DNA sites that are otherwise occluded by the histone proteins, our result suggests substantial differences between the protein search mechanism on a nucleosome performing breathing and sliding dynamics. Furthermore, we identify the molecular factors that influence the search efficiency and demonstrate how these factors together portray a highly dynamic landscape of gene regulation. Our analytical results are validated using extensive Monte Carlo simulations.
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Affiliation(s)
- Sujeet Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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5
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Mondal M, Gao YQ. Sequence‐dependent clustering properties of nucleotides fragments in an ionic solution. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202200425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology Shenzhen Bay Laboratory Shenzhen China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology Shenzhen Bay Laboratory Shenzhen China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing China
- Biomedical Pioneering Innovation Center Peking University Beijing China
- Beijing Advanced Innovation Center for Genomics Peking University Beijing China
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6
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Bernardi G. The "Genomic Code": DNA Pervasively Moulds Chromatin Structures Leaving no Room for "Junk". Life (Basel) 2021; 11:342. [PMID: 33924668 PMCID: PMC8070607 DOI: 10.3390/life11040342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two "gene spaces" were found many years ago: A GC-rich, gene-rich "genome core" and a GC-poor, gene-poor "genome desert", the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two "spatial compartments", A and B, identified on the basis of chromatin interactions; and (3) of "forests and prairies" characterized by high and low CpG islands densities. Chromatin compartments were shown to be associated with the compositionally different, flat and single- or multi-peak DNA structures of the two, GC-poor and GC-rich, "super-families" of isochores. At the second, sub-compartment, level, chromatin corresponds to flat isochores and to isochore loops (due to compositional DNA gradients) that are susceptible to extrusion. Finally, at the short-sequence level, two sets of sequences, GC-poor and GC-rich, define two different nucleosome spacings, a short one and a long one. In conclusion, chromatin structures are moulded according to a "genomic code" by DNA sequences that pervade the genome and leave no room for "junk".
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Affiliation(s)
- Giorgio Bernardi
- Science Department, Roma Tre University, Viale Marconi 446, 00146 Rome, Italy; ; Tel.: +39-33-540-5892
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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7
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Mondal M, Yang L, Cai Z, Patra P, Gao YQ. A perspective on the molecular simulation of DNA from structural and functional aspects. Chem Sci 2021; 12:5390-5409. [PMID: 34168783 PMCID: PMC8179617 DOI: 10.1039/d0sc05329e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As genetic material, DNA not only carries genetic information by sequence, but also affects biological functions ranging from base modification to replication, transcription and gene regulation through its structural and dynamic properties and variations. The motion and structural properties of DNA involved in related biological processes are also multi-scale, ranging from single base flipping to local DNA deformation, TF binding, G-quadruplex and i-motif formation, TAD establishment, compartmentalization and even chromosome territory formation, just to name a few. The sequence-dependent physical properties of DNA play vital role in all these events, and thus it is interesting to examine how simple sequence information affects DNA and the formation of the chromatin structure in these different hierarchical orders. Accordingly, molecular simulations can provide atomistic details of interactions and conformational dynamics involved in different biological processes of DNA, including those inaccessible by current experimental methods. In this perspective, which is mainly based on our recent studies, we provide a brief overview of the atomistic simulations on how the hierarchical structure and dynamics of DNA can be influenced by its sequences, base modifications, environmental factors and protein binding in the context of the protein-DNA interactions, gene regulation and structural organization of chromatin. We try to connect the DNA sequence, the hierarchical structures of DNA and gene regulation.
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Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Zhicheng Cai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China
| | - Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China.,Beijing Advanced Innovation Center for Genomics, Peking University 100871 Beijing China
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8
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Routhier E, Pierre E, Khodabandelou G, Mozziconacci J. Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics. Genome Res 2021; 31:317-326. [PMID: 33355297 PMCID: PMC7849406 DOI: 10.1101/gr.264416.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022]
Abstract
Genetically modified genomes are often used today in many areas of fundamental and applied research. In many studies, coding or noncoding regions are modified in order to change protein sequences or gene expression levels. Modifying one or several nucleotides in a genome can also lead to unexpected changes in the epigenetic regulation of genes. When designing a synthetic genome with many mutations, it would thus be very informative to be able to predict the effect of these mutations on chromatin. We develop here a deep learning approach that quantifies the effect of every possible single mutation on nucleosome positions on the full Saccharomyces cerevisiae genome. This type of annotation track can be used when designing a modified S. cerevisiae genome. We further highlight how this track can provide new insights on the sequence-dependent mechanisms that drive nucleosomes' positions in vivo.
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Affiliation(s)
- Etienne Routhier
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
| | - Edgard Pierre
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
| | | | - Julien Mozziconacci
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
- Muséum National d'Histoire Naturelle, Structure et Instabilité des Génomes, UMR7196, Paris 75231, France
- Institut Universitaire de France, Paris 75005, France
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9
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Lyubitelev AV, Kirpichnikov MP, Studitsky VM. The Role of Linker Histones in Carcinogenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Portillo-Ledesma S, Tsao LH, Wagley M, Lakadamyali M, Cosma MP, Schlick T. Nucleosome Clutches are Regulated by Chromatin Internal Parameters. J Mol Biol 2020; 433:166701. [PMID: 33181171 DOI: 10.1016/j.jmb.2020.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 01/17/2023]
Abstract
Nucleosomes cluster together when chromatin folds in the cell to form heterogeneous groups termed "clutches". These structural units add another level of chromatin regulation, for example during cell differentiation. Yet, the mechanisms that regulate their size and compaction remain obscure. Here, using our chromatin mesoscale model, we dissect clutch patterns in fibers with different combinations of nucleosome positions, linker histone density, and acetylation levels to investigate their role in clutch regulation. First, we isolate the effect of each chromatin parameter by studying systems with regular nucleosome spacing; second, we design systems with naturally-occurring linker lengths that fold onto specific clutch patterns; third, we model gene-encoding fibers to understand how these combined factors contribute to gene structure. Our results show how these chromatin parameters act together to produce different-sized nucleosome clutches. The length of nucleosome free regions (NFRs) profoundly affects clutch size, while the length of linker DNA has a moderate effect. In general, higher linker histone densities produce larger clutches by a chromatin compaction mechanism, while higher acetylation levels produce smaller clutches by a chromatin unfolding mechanism. We also show that it is possible to design fibers with naturally-occurring DNA linkers and NFRs that fold onto specific clutch patterns. Finally, in gene-encoding systems, a complex combination of variables dictates a gene-specific clutch pattern. Together, these results shed light into the mechanisms that regulate nucleosome clutches and suggest a new epigenetic mechanism by which chromatin parameters regulate transcriptional activity via the three-dimensional folded state of the genome at a nucleosome level.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, 10003, USA
| | - Lucille H Tsao
- Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, 10003, USA
| | - Meghna Wagley
- Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, 10003, USA
| | - Melike Lakadamyali
- Perelman School of Medicine, Department of Physiology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA; Perelman School of Medicine, Department of Cell and Developmental Biology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Tamar Schlick
- Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, 10003, USA; New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200062, China; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, NY, 10012, USA.
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11
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Stewart-Morgan KR, Petryk N, Groth A. Chromatin replication and epigenetic cell memory. Nat Cell Biol 2020; 22:361-371. [PMID: 32231312 DOI: 10.1038/s41556-020-0487-y] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Propagation of the chromatin landscape across cell divisions is central to epigenetic cell memory. Mechanistic analysis of the interplay between DNA replication, the cell cycle, and the epigenome has provided insights into replication-coupled chromatin assembly and post-replicative chromatin maintenance. These breakthroughs are critical for defining how proliferation impacts the epigenome during cell identity changes in development and disease. Here we review these findings in the broader context of epigenetic inheritance across mitotic cell division.
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Affiliation(s)
- Kathleen R Stewart-Morgan
- The Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,Epigenetics and Cell Fate, UMR7216 CNRS, University of Paris, Paris, France
| | - Anja Groth
- The Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
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12
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Ensembles of Breathing Nucleosomes: A Computational Study. Biophys J 2019; 118:2297-2308. [PMID: 31882248 DOI: 10.1016/j.bpj.2019.11.3395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
About three-fourths of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core. In this study, we calculate such an ensemble through a Monte Carlo simulation of a coarse-grained nucleosome model with sequence-dependent DNA mechanics. Our analysis gives detailed insights into the sequence dependence of nucleosome breathing observed in the experiment and allows us to determine the adsorption energy of the DNA bound to the protein core as a function of the ionic strength. Moreover, we predict the breathing behavior of other potentially interesting sequences and compare the findings to earlier related experiments.
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13
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Ordu O, Lusser A, Dekker NH. DNA Sequence Is a Major Determinant of Tetrasome Dynamics. Biophys J 2019; 117:2217-2227. [PMID: 31521330 PMCID: PMC6895708 DOI: 10.1016/j.bpj.2019.07.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/13/2019] [Accepted: 07/30/2019] [Indexed: 10/26/2022] Open
Abstract
Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4)2 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left- and right-handed conformations, which may prevent torque buildup in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a high-affinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono- and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono- and divalent salt concentrations counteracted this behavior. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites.
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Affiliation(s)
- Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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14
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Brehove M, Shatoff E, Donovan BT, Jipa CM, Bundschuh R, Poirier MG. DNA sequence influences hexasome orientation to regulate DNA accessibility. Nucleic Acids Res 2019; 47:5617-5633. [PMID: 31216039 PMCID: PMC6582347 DOI: 10.1093/nar/gkz283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/03/2019] [Accepted: 04/20/2019] [Indexed: 02/02/2023] Open
Abstract
Nucleosomes, the fundamental organizing units of eukaryotic genomes, contain ∼146 base pairs of DNA wrapped around a histone H3–H4 tetramer and two histone H2A–H2B dimers. Converting nucleosomes into hexasomes by removal of a H2A–H2B dimer is an important regulatory event, but its regulation and functional consequences are not well-understood. To investigate the influence of hexasomes on DNA accessibility, we used the property of the Widom-601 Nucleosome Positioning Sequence (NPS) to form homogeneously oriented hexasomes in vitro. We find that DNA accessibility to transcription factors (TF) on the hexasome H2A–H2B distal side is identical to naked DNA, while the accessibility on the H2A–H2B proximal side is reduced by 2-fold, which is due to a 2-fold reduction in hexasome unwrapping probability. We then determined that a 23 bp region of the Widom-601 NPS is responsible for forming homogeneously oriented hexasomes. Analysis of published ChIP-exo data of hexasome containing genes identified two DNA sequence motifs that correlate with hexasome orientation in vivo, while ExoIII mapping studies of these sequences revealed they generate homogeneously oriented hexasomes in vitro. These results indicate that hexasome orientation, which is influenced by the underlying DNA sequence in vivo, is important for modulating DNA accessibility to regulate transcription.
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Affiliation(s)
- Matthew Brehove
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin T Donovan
- Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Caroline M Jipa
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Department of Physics, Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA.,Division of Hematology, Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Department of Physics, Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA.,Ohio State Biochemistry Program, Ohio State University, Columbus, OH 43210, USA
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15
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Luo D, Kato D, Nogami J, Ohkawa Y, Kurumizaka H, Kono H. MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast. Nucleic Acids Res 2019; 46:7124-7137. [PMID: 29893974 PMCID: PMC6101533 DOI: 10.1093/nar/gky502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/30/2018] [Indexed: 01/06/2023] Open
Abstract
The first nucleosomes in the downstream of transcription starting sites are called +1 nucleosomes, which are expected to be readily unwrapped for DNA transcription. To investigate DNA accessibility in +1 nucleosomes, MNase-seq experiments were carried out with 20 reconstituted +1 nucleosomes of budding yeast. Although MNase has been known for its sequence preference in DNA digestions, we confirmed that this sequence preference is overwhelmed by DNA accessibility by identifying the sequence-driven and accessibility-driven cleavages. Specifically, we find that sequences favoured by MNase at the end regions such as TA dinucleotide are prohibited from cleavage at the internal sites in the early stage of digestion. Nevertheless, sequences less favoured by MNase at the end regions such as AA/TT dinucleotide are predominantly cleaved at the internal sites in the early stage of digestion. Since AA/TT is known as a rigid dinucleotide step resistant to DNA bending, these internal cleavages reflect the local site exposures induced by DNA mechanics. As the DNA entry site of +1 nucleosomes in yeast is found AA/TT-rich, this sequence element may play a role in gene activation by reducing DNA–histone affinities along the direction of DNA transcription.
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Affiliation(s)
- Di Luo
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| | - Daiki Kato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan
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16
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Onufriev AV, Schiessel H. The nucleosome: from structure to function through physics. Curr Opin Struct Biol 2019; 56:119-130. [DOI: 10.1016/j.sbi.2018.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/07/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023]
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17
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Abstract
Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the nuclear machinery. Progress in structural studies of nucleosomes and chromatin has provided detailed insight into local chromatin organization and has set the stage for recent in-depth investigations of the structural dynamics of nucleosomes and chromatin fibers. Here, we discuss the dynamic processes observed in chromatin over different length scales and timescales and review current knowledge about the biophysics of distinct structural transitions.
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Affiliation(s)
- Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael G. Poirier
- Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Graduate Program, and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210-1117, USA
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18
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Transcription shapes DNA replication initiation and termination in human cells. Nat Struct Mol Biol 2018; 26:67-77. [PMID: 30598550 PMCID: PMC6320713 DOI: 10.1038/s41594-018-0171-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/19/2018] [Indexed: 12/21/2022]
Abstract
Although DNA replication is a fundamental aspect of biology, it is not known what determines where DNA replication starts and stops in the human genome. Here we directly identify and quantitatively compare sites of replication initiation and termination in untransformed human cells. We report that replication preferentially initiates at the transcription start site of genes occupied by high levels of RNA polymerase II, and terminates at their polyadenylation sites, thus ensuring global co-directionality of transcription and replication, particularly at gene 5’ ends. During replication stress, replication initiation is stimulated downstream of genes and termination is redistributed to gene bodies; this globally re-orients replication relative to transcription around gene 3’ ends. These data suggest that replication initiation and termination are coupled to transcription in human cells, and propose a model for the impact of replication stress on genome integrity.
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19
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Tiemann-Boege I, Schwarz T, Striedner Y, Heissl A. The consequences of sequence erosion in the evolution of recombination hotspots. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0462. [PMID: 29109225 PMCID: PMC5698624 DOI: 10.1098/rstb.2016.0462] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2017] [Indexed: 12/18/2022] Open
Abstract
Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans-acting factors like PRDM9 is affected. PRDM9 is a meiosis-specific, multi-domain protein that recognizes DNA target motifs by its zinc finger domain and directs DSBs to these target sites. Here we discuss the changes in affinity of PRDM9 to eroded recognition sequences, and explain how these changes in affinity of PRDM9 can affect recombination, leading sometimes to sterility in the context of hybrid crosses. We also present experimental data showing that DNA methylation reduces PRDM9 binding in vitro. Finally, we discuss PRDM9-independent hotspots, posing the question how these hotspots evolve and change with sequence erosion. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
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Affiliation(s)
- Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Theresa Schwarz
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Angelika Heissl
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
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20
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Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV. Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core. Epigenetics Chromatin 2018; 11:11. [PMID: 29548294 PMCID: PMC5856334 DOI: 10.1186/s13072-018-0181-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/06/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Controlled modulation of nucleosomal DNA accessibility via post-translational modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs in the globular histone core-including acetylation, phosphorylation, crotonylation, propionylation, butyrylation, formylation, and citrullination-can alter the strong electrostatic interactions between the oppositely charged nucleosomal DNA and the histone proteins and thus modulate accessibility of the nucleosomal DNA, affecting processes that depend on access to the genetic information, such as transcription. However, direct experimental investigation of the effects of these PTMs is very difficult. Theoretical models can rationalize existing observations, suggest working hypotheses for future experiments, and provide a unifying framework for connecting PTMs with the observed effects. RESULTS A physics-based framework is proposed that predicts the effect of charge-altering PTMs in the histone core, quantitatively for several types of lysine charge-neutralizing PTMs including acetylation, and qualitatively for all phosphorylations, on the nucleosome stability and subsequent changes in DNA accessibility, making a connection to resulting biological phenotypes. The framework takes into account multiple partially assembled states of the nucleosome at the atomic resolution. The framework is validated against experimentally known nucleosome stability changes due to the acetylation of specific lysines, and their effect on transcription. The predicted effect of charge-altering PTMs on DNA accessibility can vary dramatically, from virtually none to a strong, region-dependent increase in accessibility of the nucleosomal DNA; in some cases, e.g., H4K44, H2AK75, and H2BK57, the effect is significantly stronger than that of the extensively studied acetylation sites such H3K56, H3K115 or H3K122. Proximity to the DNA is suggestive of the strength of the PTM effect, but there are many exceptions. For the vast majority of charge-altering PTMs, the predicted increase in the DNA accessibility should be large enough to result in a measurable modulation of transcription. However, a few possible PTMs, such as acetylation of H4K77, counterintuitively decrease the DNA accessibility, suggestive of the repressed chromatin. A structural explanation for the phenomenon is provided. For the majority of charge-altering PTMs, the effect on DNA accessibility is simply additive (noncooperative), but there are exceptions, e.g., simultaneous acetylation of H4K79 and H3K122, where the combined effect is amplified. The amplification is a direct consequence of the nucleosome-DNA complex having more than two structural states. The effect of individual PTMs is classified based on changes in the accessibility of various regions throughout the nucleosomal DNA. The PTM's resulting imprint on the DNA accessibility, "PTMprint," is used to predict effects of many yet unexplored PTMs. For example, acetylation of H4K44 yields a PTMprint similar to the PTMprint of H3K56, and thus acetylation of H4K44 is predicted to lead to a wide range of strong biological effects. CONCLUSION Charge-altering post-translational modifications in the relatively unexplored globular histone core may provide a precision mechanism for controlling accessibility to the nucleosomal DNA.
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Affiliation(s)
- Andrew T. Fenley
- Department of Physics, Virginia Tech, 2160C Torgersen Hall, Blacksburg, VA 24061 USA
| | | | - Yared H. Kidane
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
| | - Alexey V. Onufriev
- Department of Physics, Virginia Tech, 2160C Torgersen Hall, Blacksburg, VA 24061 USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061 USA
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21
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Culkin J, de Bruin L, Tompitak M, Phillips R, Schiessel H. The role of DNA sequence in nucleosome breathing. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:106. [PMID: 29185124 PMCID: PMC7001874 DOI: 10.1140/epje/i2017-11596-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/14/2017] [Indexed: 05/05/2023]
Abstract
Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence. Using a coarse-grained nucleosome model we calculate the accessibility profiles for site exposure. We find that the process is very sensitive to sequence effects, so that evolution could potentially tune the accessibility of nucleosomal DNA and would only need a small number of mutations to do so.
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Affiliation(s)
- Jamie Culkin
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Lennart de Bruin
- Laboratory for Computation and Visualization in Mathematics and Mechanics, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Marco Tompitak
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Rob Phillips
- Department of Applied Physics and Division of Biology and Biological Engineering, California Institute of Technology, 91125, Pasadena, CA, USA
| | - Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands.
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22
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A comparison of nucleosome organization in Drosophila cell lines. PLoS One 2017; 12:e0178590. [PMID: 28570602 PMCID: PMC5453549 DOI: 10.1371/journal.pone.0178590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 05/16/2017] [Indexed: 01/25/2023] Open
Abstract
Changes in the distribution of nucleosomes along the genome influence chromatin structure and impact gene expression by modulating the accessibility of DNA to transcriptional machinery. However, the role of genome-wide nucleosome positioning in gene expression and in maintaining differentiated cell states remains poorly understood. Drosophila melanogaster cell lines represent distinct tissue types and exhibit cell-type specific gene expression profiles. They thus could provide a useful tool for investigating cell-type specific nucleosome organization of an organism's genome. To evaluate this possibility, we compared genome-wide nucleosome positioning and occupancy in five different Drosophila tissue-specific cell lines, and in reconstituted chromatin, and then tested for correlations between nucleosome positioning, transcription factor binding motifs, and gene expression. Nucleosomes in all cell lines were positioned in accordance with previously known DNA-nucleosome interactions, with helically repeating A/T di-nucleotide pairs arranged within nucleosomal DNAs and AT-rich pentamers generally excluded from nucleosomal DNA. Nucleosome organization in all cell lines differed markedly from in vitro reconstituted chromatin, with highly expressed genes showing strong nucleosome organization around transcriptional start sites. Importantly, comparative analysis identified genomic regions that exhibited cell line-specific nucleosome enrichment or depletion. Further analysis of these regions identified 91 out of 16,384 possible heptamer sequences that showed differential nucleosomal occupation between cell lines, and 49 of the heptamers matched one or more known transcription factor binding sites. These results demonstrate that there is differential nucleosome positioning between these Drosophila cell lines and therefore identify a system that could be used to investigate the functional significance of differential nucleosomal positioning in cell type specification.
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23
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Winger J, Bowman GD. The Sequence of Nucleosomal DNA Modulates Sliding by the Chd1 Chromatin Remodeler. J Mol Biol 2017; 429:808-822. [PMID: 28189426 DOI: 10.1016/j.jmb.2017.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 10/20/2022]
Abstract
Chromatin remodelers are ATP-dependent enzymes that are critical for reorganizing and repositioning nucleosomes in concert with many basic cellular processes. For the chromodomain helicase DNA-binding protein 1 (Chd1) remodeler, nucleosome sliding has been shown to depend on the DNA flanking the nucleosome, transcription factor binding at the nucleosome edge, and the presence of the histone H2A/H2B dimer on the entry side. Here, we report that Chd1 is also sensitive to the sequence of DNA within the nucleosome and slides nucleosomes made with the 601 Widom positioning sequence asymmetrically. Kinetic and equilibrium experiments show that poly(dA:dT) tracts perturb remodeling reactions if within one and a half helical turns of superhelix location 2 (SHL2), where the Chd1 ATPase engages nucleosomal DNA. These sequence-dependent effects do not rely on the Chd1 DNA-binding domain and are not due to differences in nucleosome affinity. Using site-specific cross-linking, we show that internal poly(dA:dT) tracts do not block the engagement of the ATPase motor with SHL2, yet they promote multiple translational positions of DNA with respect to both Chd1 and the histone core. We speculate that Chd1 senses the sequence-dependent response of DNA as the remodeler ATPase perturbs the duplex at SHL2. These results suggest that the sequence sensitivity of histones and remodelers occur at unique segments of DNA on the nucleosome, allowing them to work together or in opposition to determine nucleosome positions throughout the genome.
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Affiliation(s)
- Jessica Winger
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregory D Bowman
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
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24
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Laxa M. Regulatory cis-elements are located in accessible promoter regions of the CAT2 promoter and affect activating histone modifications in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2017; 93:49-60. [PMID: 27734290 DOI: 10.1007/s11103-016-0546-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/20/2016] [Indexed: 05/24/2023]
Abstract
Catalase 2 (CAT2) plays an important role in the detoxification of hydrogen peroxide released either during photorespiration or as a consequence of biotic and abiotic stress as well as in the initiation of senescence. To date, our understanding of the regulation of CAT2 gene expression is rather poor. Chromatin immunoprecipitation experiments revealed that a wide region of the CAT2 promoter is nucleosome depleted, reflecting the ability to rapidly respond to changing environmental and stress conditions and, thus, adjusting the transcript levels of CAT2. The lowest nucleosome density was found in the region of -900 bp relative to the transcription initiation start (TIS) where two regulatory elements are located. The distance of the nucleosome depleted region to the TIS is quite unusual because the majority of nucleosome free regions are generally located in close vicinity to the 5' untranslated region. The analysis of transgenic 5' upstream deletion::gusA Arabidopsis lines showed that this region is important for the regulation of CAT2 promoter activity. To evaluate the function of the two motifs, the contribution of each element to CAT2 promoter activity was analyzed by site directed mutagenesis. The data revealed that the CAT2 promoter is regulated by the ACGT motif (Box2) rather than by the G-Box binding motif (Box1) in the vegetative phase of development. Furthermore, the presence of both Box1 and Box2 positively affected the abundance of activating histone modifications.
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Affiliation(s)
- Miriam Laxa
- Institute of Botany, Leibniz University Hannover, Herrenhaeuser Strasse 2, 30419, Hanover, Germany.
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25
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Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning. PLoS Pathog 2016; 12:e1006080. [PMID: 28033404 PMCID: PMC5198986 DOI: 10.1371/journal.ppat.1006080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/19/2016] [Indexed: 11/19/2022] Open
Abstract
The packaging and organization of genomic DNA into chromatin represents an additional regulatory layer of gene expression, with specific nucleosome positions that restrict the accessibility of regulatory DNA elements. The mechanisms that position nucleosomes in vivo are thought to depend on the biophysical properties of the histones, sequence patterns, like phased di-nucleotide repeats and the architecture of the histone octamer that folds DNA in 1.65 tight turns. Comparative studies of human and P. falciparum histones reveal that the latter have a strongly reduced ability to recognize internal sequence dependent nucleosome positioning signals. In contrast, the nucleosomes are positioned by AT-repeat sequences flanking nucleosomes in vivo and in vitro. Further, the strong sequence variations in the plasmodium histones, compared to other mammalian histones, do not present adaptations to its AT-rich genome. Human and parasite histones bind with higher affinity to GC-rich DNA and with lower affinity to AT-rich DNA. However, the plasmodium nucleosomes are overall less stable, with increased temperature induced mobility, decreased salt stability of the histones H2A and H2B and considerable reduced binding affinity to GC-rich DNA, as compared with the human nucleosomes. In addition, we show that plasmodium histone octamers form the shortest known nucleosome repeat length (155bp) in vitro and in vivo. Our data suggest that the biochemical properties of the parasite histones are distinct from the typical characteristics of other eukaryotic histones and these properties reflect the increased accessibility of the P. falciparum genome. Nucleosomes are not positioned randomly on DNA but on preferential sites with respect to the underlying DNA sequence. Histones belong to the most conserved eukaryotic proteins, as sequence dependent nucleosome positioning is an essential regulatory feature of nucleosomes, determining the accessibility of regulatory factors to DNA. We determined the biochemical properties of plasmodium histones and show that they are distinct from human forms, explaining the accessible chromatin structure of P. falciparum. Amino acid exchanges in the histones do not present an adaption to the AT-rich genome, but rather reduce the binding affinity to GC-rich DNA sequences, resulting in rather unstable nucleosomes with labile H2A and H2B, requiring extra-nucleosomal positioning signals to keep them on place. Plasmodium chromatin exhibits the shortest nucleosome spacing known to date potentially inhibiting the formation of higher order structures and maintaining chromatin accessible.
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26
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Torres CM, Biran A, Burney MJ, Patel H, Henser-Brownhill T, Cohen AHS, Li Y, Ben-Hamo R, Nye E, Spencer-Dene B, Chakravarty P, Efroni S, Matthews N, Misteli T, Meshorer E, Scaffidi P. The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity. Science 2016; 353:aaf1644. [PMID: 27708074 PMCID: PMC5131846 DOI: 10.1126/science.aaf1644] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 08/30/2016] [Indexed: 12/22/2022]
Abstract
Tumors comprise functionally diverse subpopulations of cells with distinct proliferative potential. Here, we show that dynamic epigenetic states defined by the linker histone H1.0 determine which cells within a tumor can sustain the long-term cancer growth. Numerous cancer types exhibit high inter- and intratumor heterogeneity of H1.0, with H1.0 levels correlating with tumor differentiation status, patient survival, and, at the single-cell level, cancer stem cell markers. Silencing of H1.0 promotes maintenance of self-renewing cells by inducing derepression of megabase-sized gene domains harboring downstream effectors of oncogenic pathways. Self-renewing epigenetic states are not stable, and reexpression of H1.0 in subsets of tumor cells establishes transcriptional programs that restrict cancer cells' long-term proliferative potential and drive their differentiation. Our results uncover epigenetic determinants of tumor-maintaining cells.
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Affiliation(s)
- Cristina Morales Torres
- Cancer Epigenetics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Alva Biran
- Department of Genetics, The Institute of Life Sciences, and The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Matthew J. Burney
- Cancer Epigenetics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Harshil Patel
- Bioinformatics, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Tristan Henser-Brownhill
- Cancer Epigenetics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Ayelet-Hashahar Shapira Cohen
- Department of Genetics, The Institute of Life Sciences, and The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB101SA, UK
| | - Rotem Ben-Hamo
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Emma Nye
- Experimental Histopathology, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Bradley Spencer-Dene
- Experimental Histopathology, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Probir Chakravarty
- Bioinformatics, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Nik Matthews
- Advanced sequencing, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Eran Meshorer
- Department of Genetics, The Institute of Life Sciences, and The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
- UCL Cancer Institute, University College London, London WC1E 6DD, UK
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27
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García-González E, Escamilla-Del-Arenal M, Arzate-Mejía R, Recillas-Targa F. Chromatin remodeling effects on enhancer activity. Cell Mol Life Sci 2016; 73:2897-910. [PMID: 27026300 PMCID: PMC11108574 DOI: 10.1007/s00018-016-2184-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/04/2016] [Accepted: 03/14/2016] [Indexed: 01/02/2023]
Abstract
During organism development, a diversity of cell types emerges with disparate, yet stable profiles of gene expression with distinctive cellular functions. In addition to gene promoters, the genome contains enhancer regulatory sequences, which are implicated in cellular specialization by facilitating cell-type and tissue-specific gene expression. Enhancers are DNA binding elements characterized by highly sophisticated and various mechanisms of action allowing for the specific interaction of general and tissue-specific transcription factors (TFs). However, eukaryotic organisms package their genetic material into chromatin, generating a physical barrier for TFs to interact with their cognate sequences. The ability of TFs to bind DNA regulatory elements is also modulated by changes in the chromatin structure, including histone modifications, histone variants, ATP-dependent chromatin remodeling, and the methylation status of DNA. Furthermore, it has recently been revealed that enhancer sequences are also transcribed into a set of enhancer RNAs with regulatory potential. These interdependent processes act in the context of a complex network of chromatin interactions, which together contributes to a renewed vision of how gene activation is coordinated in a cell-type-dependent manner. In this review, we describe the interplay between genetic and epigenetic aspects associated with enhancers and discuss their possible roles on enhancer function.
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Affiliation(s)
- Estela García-González
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México
| | - Martín Escamilla-Del-Arenal
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York City, NY, 10027, USA
| | - Rodrigo Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México.
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28
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Eslami-Mossallam B, Schiessel H, van Noort J. Nucleosome dynamics: Sequence matters. Adv Colloid Interface Sci 2016; 232:101-113. [PMID: 26896338 DOI: 10.1016/j.cis.2016.01.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 02/06/2023]
Abstract
About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming nucleosomes. Even though the histone proteins that make up the core of nucleosomes are highly conserved in evolution, nucleosomes can be very different from each other due to posttranslational modifications of the histones. Another crucial factor in making nucleosomes unique has so far been underappreciated: the sequence of their DNA. This review provides an overview of the experimental and theoretical progress that increasingly points to the importance of the nucleosomal base pair sequence. Specifically, we discuss the role of the underlying base pair sequence in nucleosome positioning, sliding, breathing, force-induced unwrapping, dissociation and partial assembly and also how the sequence can influence higher-order structures. A new view emerges: the physical properties of nucleosomes, especially their dynamical properties, are determined to a large extent by the mechanical properties of their DNA, which in turn depends on DNA sequence.
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29
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Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila. Genetics 2016; 203:219-40. [PMID: 26975664 PMCID: PMC4858776 DOI: 10.1534/genetics.116.186791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/08/2016] [Indexed: 11/18/2022] Open
Abstract
The transcription factor Suppressor of Hairless and its coactivator, the Notch intracellular domain, are polyglutamine (pQ)-rich factors that target enhancer elements and interact with other locally bound pQ-rich factors. To understand the functional repertoire of such enhancers, we identify conserved regulatory belts with binding sites for the pQ-rich effectors of both Notch and BMP/Dpp signaling, and the pQ-deficient tissue selectors Apterous (Ap), Scalloped (Sd), and Vestigial (Vg). We find that the densest such binding site cluster in the genome is located in the BMP-inducible nab locus, a homolog of the vertebrate transcriptional cofactors NAB1/NAB2 We report three major findings. First, we find that this nab regulatory belt is a novel enhancer driving dorsal wing margin expression in regions of peak phosphorylated Mad in wing imaginal discs. Second, we show that Ap is developmentally required to license the nab dorsal wing margin enhancer (DWME) to read out Notch and Dpp signaling in the dorsal compartment. Third, we find that the nab DWME is embedded in a complex of intronic enhancers, including a wing quadrant enhancer, a proximal wing disc enhancer, and a larval brain enhancer. This enhancer complex coordinates global nab expression via both tissue-specific activation and interenhancer silencing. We suggest that DWME integration of BMP signaling maintains nab expression in proliferating margin descendants that have divided away from Notch-Delta boundary signaling. As such, uniform expression of genes like nab and vestigial in proliferating compartments would typically require both boundary and nonboundary lineage-specific enhancers.
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Kakou B, Angers B, Glémet H. Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens). Genome 2016; 59:149-58. [PMID: 26841134 DOI: 10.1139/gen-2015-0114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The intergenic spacer (IGS) is located between ribosomal RNA (rRNA) gene copies. Within the IGS, regulatory elements for rRNA gene transcription are found, as well as a varying number of other repetitive elements that are at the root of IGS length heterogeneity. This heterogeneity has been shown to have a functional significance through its effect on growth rate. Here, we present the structural organization of yellow perch (Perca flavescens) IGS based on its entire sequence, as well as the IGS length variation within a natural population. Yellow perch IGS structure has four discrete regions containing tandem repeat elements. For three of these regions, no specific length class was detected as allele size was seemingly normally distributed. However, for one repeat region, PCR amplification uncovered the presence of two distinctive IGS variants representing a length difference of 1116 bp. This repeat region was also devoid of any CpG sites despite a high GC content. Balanced selection may be holding the alleles in the population and would account for the high diversity of length variants observed for adjacent regions. Our study is an important precursor for further work aiming to assess the role of IGS length variation in influencing growth rate in fish.
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Affiliation(s)
- Bidénam Kakou
- a Département des sciences de l'environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Bernard Angers
- b Department of Biological Sciences, Université de Montréal, Montréal, QC H3C 3J7, Canada.,c GRIL - Groupe de recherche interuniversitaire en limnologie et en environnement aquatique
| | - Hélène Glémet
- a Département des sciences de l'environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada.,c GRIL - Groupe de recherche interuniversitaire en limnologie et en environnement aquatique
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Promoter and Terminator Discovery and Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:21-44. [PMID: 27277391 DOI: 10.1007/10_2016_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Control of gene expression is crucial to optimize metabolic pathways and synthetic gene networks. Promoters and terminators are stretches of DNA upstream and downstream (respectively) of genes that control both the rate at which the gene is transcribed and the rate at which mRNA is degraded. As a result, both of these elements control net protein expression from a synthetic construct. Thus, it is highly important to discover and engineer promoters and terminators with desired characteristics. This chapter highlights various approaches taken to catalogue these important synthetic elements. Specifically, early strategies have focused largely on semi-rational techniques such as saturation mutagenesis to diversify native promoters and terminators. Next, in an effort to reduce the length of the synthetic biology design cycle, efforts in the field have turned towards the rational design of synthetic promoters and terminators. In this vein, we cover recently developed methods such as hybrid engineering, high throughput characterization, and thermodynamic modeling which allow finer control in the rational design of novel promoters and terminators. Emphasis is placed on the methodologies used and this chapter showcases the utility of these methods across multiple host organisms.
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Balliano AJ, Hayes JJ. Base excision repair in chromatin: Insights from reconstituted systems. DNA Repair (Amst) 2015; 36:77-85. [PMID: 26411876 DOI: 10.1016/j.dnarep.2015.09.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The process of base excision repair has been completely reconstituted in vitro and structural and biochemical properties of the component enzymes thoroughly studied on naked DNA templates. More recent work in this field aims to understand how BER operates on the natural substrate, chromatin [1,2]. Toward this end, a number of researchers, including the Smerdon group, have focused attention to understand how individual enzymes and reconstituted BER operate on nucleosome substrates. While nucleosomes were once thought to completely restrict access of DNA-dependent factors, the surprising finding from these studies suggests that at least some BER components can utilize target DNA bound within nucleosomes as substrates for their enzymatic processes. This data correlates well with both structural studies of these enzymes and our developing understanding of nucleosome conformation and dynamics. While more needs to be learned, these studies highlight the utility of reconstituted BER and chromatin systems to inform our understanding of in vivo biological processes.
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Affiliation(s)
- Angela J Balliano
- University of Rochester Medical Center, 601 Elmwood Ave., Box 712, Rochester, NY 14642, United States
| | - Jeffrey J Hayes
- University of Rochester Medical Center, 601 Elmwood Ave., Box 712, Rochester, NY 14642, United States.
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GAA triplet-repeats cause nucleosome depletion in the human genome. Genomics 2015; 106:88-95. [DOI: 10.1016/j.ygeno.2015.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 11/18/2022]
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Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo. G3-GENES GENOMES GENETICS 2015; 5:1889-97. [PMID: 26175451 PMCID: PMC4555225 DOI: 10.1534/g3.115.020271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Packaging of genomic DNA into nucleosomes is nearly universally conserved in eukaryotes, and many features of the nucleosome landscape are quite conserved. Nonetheless, quantitative aspects of nucleosome packaging differ between species because, for example, the average length of linker DNA between nucleosomes can differ significantly even between closely related species. We recently showed that the difference in nucleosome spacing between two Hemiascomycete species—Saccharomyces cerevisiae and Kluyveromyces lactis—is established by trans-acting factors rather than being encoded in cis in the DNA sequence. Here, we generated several S. cerevisiae strains in which endogenous copies of candidate nucleosome spacing factors are deleted and replaced with the orthologous factors from K. lactis. We find no change in nucleosome spacing in such strains in which H1 or Isw1 complexes are swapped. In contrast, the K. lactis gene encoding the ATP-dependent remodeler Chd1 was found to direct longer internucleosomal spacing in S. cerevisiae, establishing that this remodeler is partially responsible for the relatively long internucleosomal spacing observed in K. lactis. By analyzing several chimeric proteins, we find that sequence differences that contribute to the spacing activity of this remodeler are dispersed throughout the coding sequence, but that the strongest spacing effect is linked to the understudied N-terminal end of Chd1. Taken together, our data find a role for sequence evolution of a chromatin remodeler in establishing quantitative aspects of the chromatin landscape in a species-specific manner.
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Unraveling determinants of transcription factor binding outside the core binding site. Genome Res 2015; 25:1018-29. [PMID: 25762553 PMCID: PMC4484385 DOI: 10.1101/gr.185033.114] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 03/04/2015] [Indexed: 11/25/2022]
Abstract
Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the characterization of sequence motifs recognized by TFs, our ability to quantitatively predict TF binding to different regulatory sequences is still limited. Here, we present a novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment. Applying this binding assay to two yeast TFs, we demonstrate that sequences outside the core TF binding site profoundly affect TF binding. We show that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured differential TF binding. We further characterize the dependence of TF binding, accounting for measurements of single and co-occurring binding events, on the number and location of binding sites and on the TF concentration. Finally, by coupling our in vitro TF binding measurements, and another application of our method probing nucleosome formation, to in vivo expression measurements carried out with the same template sequences serving as promoters, we offer insights into mechanisms that may determine the different expression outcomes observed. Our assay thus paves the way to a more comprehensive understanding of TF binding to regulatory sequences and allows the characterization of TF binding determinants within and outside of core binding sites.
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Wang J, Place RF, Portnoy V, Huang V, Kang MR, Kosaka M, Ho MKC, Li LC. Inducing gene expression by targeting promoter sequences using small activating RNAs. J Biol Methods 2015; 2. [PMID: 25839046 DOI: 10.14440/jbm.2015.39] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vector-based systems comprised of exogenous nucleic acid sequences remain the standard for ectopic expression of a particular gene. Such systems offer robust overexpression, but have inherent drawbacks such as the tedious process of construction, excluding sequences (e.g. introns and untranslated regions) important for gene function and potential insertional mutagenesis of host genome associated with the use of viral vectors. We and others have recently reported that short double-stranded RNAs (dsRNAs) can induce endogenous gene expression by targeting promoter sequences in a phenomenon referred to as RNA activation (RNAa) and such dsRNAs are termed small activating RNAs (saRNAs). To date, RNAa has been successfully utilized to induce the expression of different genes such as tumor suppressor genes. Here, we describe a detailed protocol for target selection and dsRNA design with associated experiments to facilitate RNAa in cultured cells. This technique may be applied to selectively activate endogenous gene expression for studying gene function, interrogating molecular pathways and reprogramming cell fate.
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Affiliation(s)
- Ji Wang
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Robert F Place
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Victoria Portnoy
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Vera Huang
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Moo Rim Kang
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mika Kosaka
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Maurice Kwok Chung Ho
- Biotechnology Research Institute and Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Long-Cheng Li
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.,Laboratory of Molecular Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Lenz L, Hoenderdos M, Prinsen P, Schiessel H. The influence of DNA shape fluctuations on fluorescence resonance energy transfer efficiency measurements in nucleosomes. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064104. [PMID: 25564291 DOI: 10.1088/0953-8984/27/6/064104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fluorescence resonance energy transfer (FRET) measurements allow one to observe site exposure in nucleosomes, i.e. the transient unwrapping of a part of the wrapped DNA from the histone octamer. In such experiments one can typically distinguish between a closed state and an open state but in principle one might hope to detect several states, each corresponding to a certain number of open binding sites. Here we show that even in an ideal FRET setup it would be hard to detect unwrapping states with intermediate levels of FRET efficiencies. As the unwrapped DNA molecule, modelled here as a wormlike chain, has a finite stiffness, shape fluctuations smear out FRET signals completely from such intermediate states.
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Affiliation(s)
- Lucia Lenz
- Instituut-Lorentz, Leiden University, PO Box 9506, 2300 RA Leiden, The Netherlands. Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstr. 19, 79104 Freiburg im Breisgau, Germany
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Abstract
Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. This review by Iwafuchi-Doi and Zaret focuses on the most recent studies of pioneer factors in cell programming and reprogramming, how pioneer factors have special chromatin-binding properties, and facilitators and impediments to chromatin binding. A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in “closed” chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Abe H, Gemmell NJ. Abundance, arrangement, and function of sequence motifs in the chicken promoters. BMC Genomics 2014; 15:900. [PMID: 25318583 PMCID: PMC4203960 DOI: 10.1186/1471-2164-15-900] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 10/08/2014] [Indexed: 01/01/2023] Open
Abstract
Background Eukaryotic promoters are regions containing various sequence motifs necessary to control gene transcription. Much evidence has emerged showing that structural and/or contextual changes in regulatory elements can critically affect cis-regulatory activity. As sequence motifs can be key factors in maintaining complex promoter architectures, one effective approach to further understand the evolution of promoter regions in vertebrates is to compare the abundance and distribution patterns of sequence motifs in these regions between divergent species. When compared with mammals, the chicken (Gallus gallus) has a very different genome composition and sufficient genomic information to make it a good model for the exploration of promoter structure and evolution. Results More than 10% of chicken genes contained short tandem repeat (STR) in the region 2 kb upstream of promoters, but the total number of STRs observed in chicken is approximately half of that detected in human promoters. In terms of the STR motif frequencies, chicken promoter regions were more similar to other avian and mammalian promoters than these were to the entire chicken genome. Unlike other STRs, nearly half of the trinucleotide repeats found in promoters partly or entirely overlapped with CpG islands, indicating potential association with nucleosome positions. Moreover, the chicken promoters are abundant with sequence motifs such as poly-A, poly-G and G-quadruplexes, especially in the core region, that are otherwise rare in the genome. Most of sequence motifs showed strong functional enrichment for particular gene ontology (GO) categories, indicating roles in regulation of transcription and gene expression, as well as immune response and cognition. Conclusions Chicken promoter regions share some, but not all, of the structural features observed in mammalian promoters. The findings presented here provide empirical evidence suggesting that the frequencies and locations of STR motifs have been conserved through promoter evolution in a lineage-specific manner. Correlation analysis between GO categories and sequence motifs suggests motif-specific constraints acting on gene function. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-900) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand.
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Linnertz C, Anderson L, Gottschalk W, Crenshaw D, Lutz MW, Allen J, Saith S, Mihovilovic M, Burke JR, Welsh-Bohmer KA, Roses AD, Chiba-Falek O. The cis-regulatory effect of an Alzheimer's disease-associated poly-T locus on expression of TOMM40 and apolipoprotein E genes. Alzheimers Dement 2014; 10:541-51. [PMID: 24439168 PMCID: PMC4098029 DOI: 10.1016/j.jalz.2013.08.280] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 05/13/2013] [Accepted: 08/06/2013] [Indexed: 12/19/2022]
Abstract
BACKGROUND We investigated the genomic region spanning the Translocase of the Outer Mitochondrial Membrane 40-kD (TOMM40) and Apolipoprotein E (APOE) genes, that has been associated with the risk and age of onset of late-onset Alzheimer's disease (LOAD) to determine whether a highly polymorphic, intronic poly-T within this region (rs10524523; hereafter, 523) affects expression of the APOE and TOMM40 genes. Alleles of this locus are classified as S, short; L, long; and VL, very long based on the number of T residues. METHODS We evaluated differences in APOE messenger RNA (mRNA) and TOMM40 mRNA levels as a function of the 523 genotype in two brain regions from APOE ε3/ε3 white autopsy-confirmed LOAD cases and normal controls. We further investigated the effect of the 523 locus in its native genomic context using a luciferase expression system. RESULTS The expression of both genes was significantly increased with disease. Mean expression of APOE and TOMM40 mRNA levels were higher in VL homozygotes compared with S homozygotes in the temporal and occipital cortexes from normal and LOAD cases. Results of a luciferase reporter system were consistent with the human brain mRNA analysis; the 523 VL poly-T resulted in significantly higher expression than the S poly-T. Although the effect of poly-T length on reporter expression was the same in HepG2 hepatoma and SH-SY5Y neuroblastoma cells, the magnitude of the effect was greater in the neuroblastoma than in the hepatoma cells, which implies tissue-specific modulation of the 523 poly-T. CONCLUSIONS These results suggest that the 523 locus may contribute to LOAD susceptibility by modulating the expression of TOMM40 and/or APOE transcription.
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Affiliation(s)
- Colton Linnertz
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lauren Anderson
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - William Gottschalk
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA; Division of Neurology, Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA
| | - Donna Crenshaw
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA; Division of Neurology, Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA
| | - Michael W Lutz
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA; Division of Neurology, Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA
| | - Jawara Allen
- Institute for Genome Sciences & Policy, Duke University Medical Center, Durham, NC, USA
| | - Sunita Saith
- Institute for Genome Sciences & Policy, Duke University Medical Center, Durham, NC, USA
| | - Mirta Mihovilovic
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - James R Burke
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA; Division of Neurology, Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA
| | - Kathleen A Welsh-Bohmer
- Division of Neurology, Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA
| | - Allen D Roses
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA; Division of Neurology, Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA; Zinfandel Pharmaceuticals, Chapel Hill, NC, USA
| | - Ornit Chiba-Falek
- Division of Neurology at the Department of Medicine, Duke University Medical Center, Durham, NC, USA; Division of Neurology, Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA; Institute for Genome Sciences & Policy, Duke University Medical Center, Durham, NC, USA.
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Shi J, Zheng M, Ye Y, Li M, Chen X, Hu X, Sun J, Zhang X, Jiang C. Drosophila Brahma complex remodels nucleosome organizations in multiple aspects. Nucleic Acids Res 2014; 42:9730-9. [PMID: 25081211 PMCID: PMC4150808 DOI: 10.1093/nar/gku717] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
ATP-dependent chromatin remodeling complexes regulate nucleosome organizations. In Drosophila, gene Brm encodes the core Brahma complex, the ATPase subunit of SWI/SNF class of chromatin remodelers. Its role in modulating the nucleosome landscape in vivo is unclear. In this study, we knocked down Brm in Drosophila third instar larvae to explore the changes in nucleosome profiles and global gene transcription. The results show that Brm knockdown leads to nucleosome occupancy changes throughout the entire genome with a bias in occupancy decrease. In contrast, the knockdown has limited impacts on nucleosome position shift. The knockdown also alters another important physical property of nucleosome positioning, fuzziness. Nucleosome position shift, gain or loss and fuzziness changes are all enriched in promoter regions. Nucleosome arrays around the 5' ends of genes are reorganized in five patterns as a result of Brm knockdown. Intriguingly, the concomitant changes in the genes adjacent to the Brahma-dependent remodeling regions have important roles in development and morphogenesis. Further analyses reveal abundance of AT-rich motifs for transcription factors in the remodeling regions.
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Affiliation(s)
- Jiejun Shi
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Meizhu Zheng
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Youqiong Ye
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Min Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaolong Chen
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xinjie Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jin Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaobai Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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Bunnik EM, Polishko A, Prudhomme J, Ponts N, Gill SS, Lonardi S, Le Roch KG. DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum. BMC Genomics 2014; 15:347. [PMID: 24885191 PMCID: PMC4035074 DOI: 10.1186/1471-2164-15-347] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/30/2014] [Indexed: 12/11/2022] Open
Abstract
Background In eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relatively few transcription factors, while extensive nucleosome remodeling occurs during its replicative cycle in red blood cells. These observations point towards an important role of the nucleosome landscape in regulating gene expression. However, the relation between nucleosome positioning and transcriptional activity has thus far not been explored in detail in the parasite. Results Here, we analyzed nucleosome positioning in the asexual and sexual stages of the parasite’s erythrocytic cycle using chromatin immunoprecipitation of MNase-digested chromatin, followed by next-generation sequencing. We observed a relatively open chromatin structure at the trophozoite and gametocyte stages, consistent with high levels of transcriptional activity in these stages. Nucleosome occupancy of genes and promoter regions were subsequently compared to steady-state mRNA expression levels. Transcript abundance showed a strong inverse correlation with nucleosome occupancy levels in promoter regions. In addition, AT-repeat sequences were strongly unfavorable for nucleosome binding in P. falciparum, and were overrepresented in promoters of highly expressed genes. Conclusions The connection between chromatin structure and gene expression in P. falciparum shares similarities with other eukaryotes. However, the remarkable nucleosome dynamics during the erythrocytic stages and the absence of a large variety of transcription factors may indicate that nucleosome binding and remodeling are critical regulators of transcript levels. Moreover, the strong dependency between chromatin structure and DNA sequence suggests that the P. falciparum genome may have been shaped by nucleosome binding preferences. Nucleosome remodeling mechanisms in this deadly parasite could thus provide potent novel anti-malarial targets. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-347) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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Affiliation(s)
- Amanda L. Hughes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
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Pascuzzi PE, Flores-Vergara MA, Lee TJ, Sosinski B, Vaughn MW, Hanley-Bowdoin L, Thompson WF, Allen GC. In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts. THE PLANT CELL 2014; 26:102-20. [PMID: 24488963 PMCID: PMC3963562 DOI: 10.1105/tpc.113.121194] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 11/25/2013] [Accepted: 01/10/2014] [Indexed: 05/21/2023]
Abstract
Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.
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Affiliation(s)
- Pete E. Pascuzzi
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Tae-Jin Lee
- Department of Plant Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Bryon Sosinski
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Linda Hanley-Bowdoin
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - William F. Thompson
- Departments of Plant Biology, Genetics, and Crop Science, North Carolina State University, Raleigh, North Carolina 27695
| | - George C. Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695
- Address correspondence to
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45
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Chiba S, Tsuchiya N, Horikawa Y, Narita S, Inoue T, Akihama S, Saito M, Numakura K, Tsuruta H, Huang M, Satoh S, Habuchi T. Functional mononucleotide repeat polymorphism in the promoter region of HGF is associated with risk and malignant aggressiveness of bladder cancer. Int J Oncol 2013; 44:678-84. [PMID: 24366484 DOI: 10.3892/ijo.2013.2221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/18/2013] [Indexed: 11/05/2022] Open
Abstract
Increased expression of hepatocyte growth factor (HGF) has been shown to be associated with aggressiveness in several types of cancer. Shorter variants of deoxyadenosine tract element (DATE) located in the HGF promoter region have been reported to enhance the expression of HGF. In this study, we investigated the role of HGF DATE variants in bladder cancer risk, HGF expression and clinicopathological features. The frequency of individuals with a short DATE (<28 repeats) in peripheral blood lymphocytes (PBLs) was significantly higher in bladder cancer patients compared to controls (p<0.001). Somatic mutations were observed in 37 of 70 bladder tumor (BT) tissues and the frequency of mutation to long DATE was significantly higher than that to short DATE (p=0.047). The presence of the short DATE in BT tissue was significantly associated with higher tumor grade (p=0.015). HGF mRNA levels were significantly higher in pT2 tumors than pTa or pT1 tumors (p=0.019), and in grade 3 tumors than grade 1 or 2 tumors (p=0.020). Furthermore, BT tissues with the short DATE showed significantly higher levels of HGF mRNA (p<0.001). In patients who underwent radical cystectomy, those with higher HGF expression had a significantly shorter overall survival than those with lower HGF expression (p=0.012). In conclusion, HGF may be associated with the prognosis of patients who undergo radical cystectomy, and the HGF DATE may affect the risk and aggressiveness of bladder cancer by altering HGF expression.
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Affiliation(s)
- Syuji Chiba
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Norihiko Tsuchiya
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Yohei Horikawa
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Shintaro Narita
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Takamitsu Inoue
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Susumu Akihama
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Mitsuru Saito
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Kazuyuki Numakura
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroshi Tsuruta
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Mingguo Huang
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Shigeru Satoh
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Tomonori Habuchi
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
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46
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Rube HT, Song JS. Quantifying the role of steric constraints in nucleosome positioning. Nucleic Acids Res 2013; 42:2147-58. [PMID: 24288372 PMCID: PMC3936764 DOI: 10.1093/nar/gkt1239] [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] [Indexed: 01/02/2023] Open
Abstract
Statistical positioning, the localization of nucleosomes packed against a fixed barrier, is conjectured to explain the array of well-positioned nucleosomes at the 5′ end of genes, but the extent and precise implications of statistical positioning in vivo are unclear. We examine this hypothesis quantitatively and generalize the idea to include moving barriers as well as nucleosomes actively packed against a barrier. Early experiments noted a similarity between the nucleosome profile aligned and averaged across genes and that predicted by statistical positioning; however, we demonstrate that aligning random nucleosomes also generates the same profile, calling the previous interpretation into question. New rigorous results reformulate statistical positioning as predictions on the variance structure of nucleosome locations in individual genes. In particular, a quantity termed the variance gradient, describing the change in variance between adjacent nucleosomes, is tested against recent high-throughput nucleosome sequencing data. Constant variance gradients provide support for generalized statistical positioning in ∼50% of long genes. Genes that deviate from predictions have high nucleosome turnover and cell-to-cell gene expression variability. The observed variance gradient suggests an effective nucleosome size of 158 bp, instead of the commonly perceived 147 bp. Our analyses thus clarify the role of statistical positioning in vivo.
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Affiliation(s)
- H Tomas Rube
- Institute for Human Genetics, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA, Department of Epidemiology and Biostatistics, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA and Department of Bioengineering and Therapeutic Sciences, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA
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Johnson S, Chen YJ, Phillips R. Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping. PLoS One 2013; 8:e75799. [PMID: 24146776 PMCID: PMC3795714 DOI: 10.1371/journal.pone.0075799] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/19/2013] [Indexed: 01/31/2023] Open
Abstract
Large-scale DNA deformation is ubiquitous in transcriptional regulation in prokaryotes and eukaryotes alike. Though much is known about how transcription factors and constellations of binding sites dictate where and how gene regulation will occur, less is known about the role played by the intervening DNA. In this work we explore the effect of sequence flexibility on transcription factor-mediated DNA looping, by drawing on sequences identified in nucleosome formation and ligase-mediated cyclization assays as being especially favorable for or resistant to large deformations. We examine a poly(dA:dT)-rich, nucleosome-repelling sequence that is often thought to belong to a class of highly inflexible DNAs; two strong nucleosome positioning sequences that share a set of particular sequence features common to nucleosome-preferring DNAs; and a CG-rich sequence representative of high G+C-content genomic regions that correlate with high nucleosome occupancy in vivo. To measure the flexibility of these sequences in the context of DNA looping, we combine the in vitro single-molecule tethered particle motion assay, a canonical looping protein, and a statistical mechanical model that allows us to quantitatively relate the looping probability to the looping free energy. We show that, in contrast to the case of nucleosome occupancy, G+C content does not positively correlate with looping probability, and that despite sharing sequence features that are thought to determine nucleosome affinity, the two strong nucleosome positioning sequences behave markedly dissimilarly in the context of looping. Most surprisingly, the poly(dA:dT)-rich DNA that is often characterized as highly inflexible in fact exhibits one of the highest propensities for looping that we have measured. These results argue for a need to revisit our understanding of the mechanical properties of DNA in a way that will provide a basis for understanding DNA deformation over the entire range of biologically relevant scenarios that are impacted by DNA deformability.
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Affiliation(s)
- Stephanie Johnson
- Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Yi-Ju Chen
- Department of Physics, California Institute of Technology, Pasadena, California, United States of America
| | - Rob Phillips
- Departments of Applied Physics and Biology, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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Nalabothula N, Xi L, Bhattacharyya S, Widom J, Wang JP, Reeve JN, Santangelo TJ, Fondufe-Mittendorf YN. Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs. BMC Genomics 2013; 14:391. [PMID: 23758892 PMCID: PMC3691661 DOI: 10.1186/1471-2164-14-391] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/31/2013] [Indexed: 02/03/2023] Open
Abstract
Background Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code. Results Eukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription. Conclusions The results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes.
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Affiliation(s)
- Narasimharao Nalabothula
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C. A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. PLoS Genet 2013; 9:e1003479. [PMID: 23658529 PMCID: PMC3642058 DOI: 10.1371/journal.pgen.1003479] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 03/12/2013] [Indexed: 11/30/2022] Open
Abstract
Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology, and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors, including the CAF-1 complex, Spt10, and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning, and these data provide a valuable resource for future studies. The genome in eukaryotic cells is packaged into nucleosomes, which play critical roles in regulating where and when different genes are expressed. For example, nucleosomes can physically block access of transcription factor to sites on DNA or direct regulatory proteins to DNA. Consistent with these roles, nucleosomes assume a stereotypical pattern around genes: they are depleted at the promoter region that marks the start of genes and assume a regularly spaced array within genes. To identify factors involved in this organization, we generated high-resolution nucleosome and transcriptome maps for 50 loss-of-function mutants with known or suspected roles in nucleosome biology in budding yeast. We show that nucleosome organization is determined by the combined effects of many factors that often exert opposing forces on nucleosomes. We further demonstrate that specific nucleosomes can be positioned independently within genes and that repositioning of nucleosomes at the start of genes may affect expression of these genes in response to environmental stimuli. Data mining of this extensive resource allowed us to show that general transcription factors act as insulators at diverging promoters to prevent the formation of cryptic transcripts, and also revealed 36 novel transcripts regulated by the Tup1/Cyc8 complex.
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Affiliation(s)
- Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kyle Tsui
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Sanie Mnaimneh
- Department of Medical Research, Banting and Best, Toronto, Ontario, Canada
| | - Timothy R. Hughes
- Department of Medical Research, Banting and Best, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Corey Nislow
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
- Department of Medical Research, Banting and Best, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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50
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Labonne JDJ, Dorweiler JE, McGinnis KM. Changes in nucleosome position at transcriptional start sites of specific genes in Zea mays mediator of paramutation1 mutants. Epigenetics 2013; 8:398-408. [PMID: 23538550 PMCID: PMC3674049 DOI: 10.4161/epi.24199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nucleosomes facilitate compaction of DNA within the confines of the eukaryotic nucleus. This packaging of DNA and histone proteins must accommodate cellular processes, such as transcription and DNA replication. The repositioning of nucleosomes to facilitate cellular processes is likely regulated by several factors. In Zea mays, Mediator of paramutation1 (MOP1) has been demonstrated to be an epigenetic regulator of gene expression. Based on sequence orthology and mutant phenotypes, MOP1 is likely to function in an RNA-dependent pathway to mediate changes to chromatin. High-resolution microarrays were used to assay the distribution of nucleosomes across the transcription start sites (TSSs) of ~400 maize genes in wild type and mutant mop1-1 tissues. Analysis of nucleosome distribution in leaf, immature tassel and ear shoot tissues resulted in the identification of three genes showing consistent differences in nucleosome positioning and occupancy between wild type and mutant mop1-1. These specific changes in nucleosome distribution were located upstream as well as downstream of the TSS. No direct relationship between the specific changes in nucleosome distribution and transcription were observed through quantitative expression analysis in these tissues. In silico prediction suggests that nucleosome positioning is not dictated by intrinsic DNA sequence signals in the TSSs of two of the identified genes, suggesting a role for chromatin remodeling proteins in MOP1-mediated pathways. These results also indicate that MOP1 contributions to nucleosome position may be either separate from changes in gene expression, or cooperative with development and other levels of regulation in coordinating gene expression.
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Affiliation(s)
| | - Jane E Dorweiler
- Department of Biological Sciences; Marquette University; Milwaukee, WI USA
| | - Karen M McGinnis
- Department of Biological Science; Florida State University; Tallahassee, FL USA
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