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Korolev N, Zinchenko A, Soman A, Chen Q, Wong SY, Berezhnoy NV, Basak R, van der Maarel JRC, van Noort J, Nordenskiöld L. Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters. Sci Rep 2022; 12:15558. [PMID: 36114220 PMCID: PMC9481575 DOI: 10.1038/s41598-022-19471-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/30/2022] [Indexed: 11/14/2022] Open
Abstract
Large topologically associated domains (TADs) contain irregularly spaced nucleosome clutches, and interactions between such clutches are thought to aid the compaction of these domains. Here, we reconstituted TAD-sized chromatin fibers containing hundreds of nucleosomes on native source human and lambda-phage DNA and compared their mechanical properties at the single-molecule level with shorter ‘601’ arrays with various nucleosome repeat lengths. Fluorescent imaging showed increased compaction upon saturation of the DNA with histones and increasing magnesium concentration. Nucleosome clusters and their structural fluctuations were visualized in confined nanochannels. Force spectroscopy revealed not only similar mechanical properties of the TAD-sized fibers as shorter fibers but also large rupture events, consistent with breaking the interactions between distant clutches of nucleosomes. Though the arrays of native human DNA, lambda-phage and ‘601’ DNA featured minor differences in reconstitution yield and nucleosome stability, the fibers’ global structural and mechanical properties were similar, including the interactions between nucleosome clutches. These single-molecule experiments quantify the mechanical forces that stabilize large TAD-sized chromatin domains consisting of disordered, dynamically interacting nucleosome clutches and their effect on the condensation of large chromatin domains.
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2
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Smith CEL, Whitehouse LLE, Poulter JA, Wilkinson Hewitt L, Nadat F, Jackson BR, Manfield IW, Edwards TA, Rodd HD, Inglehearn CF, Mighell AJ. A missense variant in specificity protein 6 (SP6) is associated with amelogenesis imperfecta. Hum Mol Genet 2021; 29:1417-1425. [PMID: 32167558 PMCID: PMC7268548 DOI: 10.1093/hmg/ddaa041] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 01/01/2023] Open
Abstract
Amelogenesis is the process of enamel formation. For amelogenesis to proceed, the cells of the inner enamel epithelium (IEE) must first proliferate and then differentiate into the enamel-producing ameloblasts. Amelogenesis imperfecta (AI) is a heterogeneous group of genetic conditions that result in defective or absent tooth enamel. We identified a 2 bp variant c.817_818GC>AA in SP6, the gene encoding the SP6 transcription factor, in a Caucasian family with autosomal dominant hypoplastic AI. The resulting missense protein change, p.(Ala273Lys), is predicted to alter a DNA-binding residue in the first of three zinc fingers. SP6 has been shown to be crucial to both proliferation of the IEE and to its differentiation into ameloblasts. SP6 has also been implicated as an AI candidate gene through its study in rodent models. We investigated the effect of the missense variant in SP6 (p.(Ala273Lys)) using surface plasmon resonance protein-DNA binding studies. We identified a potential SP6 binding motif in the AMBN proximal promoter sequence and showed that wild-type (WT) SP6 binds more strongly to it than the mutant protein. We hypothesize that SP6 variants may be a very rare cause of AI due to the critical roles of SP6 in development and that the relatively mild effect of the missense variant identified in this study is sufficient to affect amelogenesis causing AI, but not so severe as to be incompatible with life. We suggest that current AI cohorts, both with autosomal recessive and dominant disease, be screened for SP6 variants.
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Affiliation(s)
- Claire E L Smith
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Laura L E Whitehouse
- School of Dentistry, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9LU, UK
| | - James A Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Laura Wilkinson Hewitt
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Fatima Nadat
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Brian R Jackson
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Iain W Manfield
- Centre for Biomolecular Interactions Technology Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds LS2 9JT, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Helen D Rodd
- Academic Unit of Oral Health Dentistry and Society, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Chris F Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Alan J Mighell
- School of Dentistry, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9LU, UK
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3
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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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Varizhuk A, Isaakova E, Pozmogova G. DNA G-Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling: Transient Genomic G4s Assist in the Establishment and Maintenance of Epigenetic Marks, While Persistent G4s May Erase Epigenetic Marks. Bioessays 2019; 41:e1900091. [PMID: 31379012 DOI: 10.1002/bies.201900091] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/09/2019] [Indexed: 01/07/2023]
Abstract
Here, the emerging data on DNA G-quadruplexes (G4s) as epigenetic modulators are reviewed and integrated. This concept has appeared and evolved substantially in recent years. First, persistent G4s (e.g., those stabilized by exogenous ligands) were linked to the loss of the histone code. More recently, transient G4s (i.e., those formed upon replication or transcription and unfolded rapidly by helicases) were implicated in CpG island methylation maintenance and de novo CpG methylation control. The most recent data indicate that there are direct interactions between G4s and chromatin remodeling factors. Finally, multiple findings support the indirect participation of G4s in chromatin reshaping via interactions with remodeling-related transcription factors (TFs) or damage responders. Here, the links between the above processes are analyzed; also, how further elucidation of these processes may stimulate the progress of epigenetic therapy is discussed, and the remaining open questions are highlighted.
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Affiliation(s)
- Anna Varizhuk
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Ekaterina Isaakova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Galina Pozmogova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
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5
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Ming Z, Chen Q, Chen N, Lin M, Liu N, Hu J, Xiao X. Eliminating the secondary structure of targeting strands for enhancement of DNA probe based low-abundance point mutation detection. Anal Chim Acta 2019; 1075:137-143. [PMID: 31196419 DOI: 10.1016/j.aca.2019.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 10/26/2022]
Abstract
Nucleic acid probes are very useful tools in biological and medical science. However, the essential sensing mechanism of nucleic acid probes was prone to the interference of surrounding sequences. Especially when the target sequences formed secondary structures such as hairpin or quadruplex, the nucleic acid probes were hindered from hybridizing with target strands, greatly disabled the function of probes. Herein, we have established an Open strand based strategy for eliminating the influence of secondary structures on the performance of nucleic acid probes. The strategy was general toward different lengths, secondary structures and sequences of the targeting strand, and we found that the improvement was higher when the secondary structure of the targeting strand was more complicated. Experiments on synthetic single stranded DNA and real clinical genomic DNA samples were conducted for low abundance mutation detection, and the limit of detection for TERT-C228T and BRCA2 rs80359065 mutations could be 0.02% and 0.05% respectively, demonstrating the clinical practicability of our proposed strategy in low abundance mutation detection.
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Affiliation(s)
- Zhihao Ming
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Qianzhi Chen
- Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Chen
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Meng Lin
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Liu
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Junbo Hu
- Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China.
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6
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Greiff V, Weber CR, Palme J, Bodenhofer U, Miho E, Menzel U, Reddy ST. Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires. THE JOURNAL OF IMMUNOLOGY 2017; 199:2985-2997. [DOI: 10.4049/jimmunol.1700594] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/16/2017] [Indexed: 11/19/2022]
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Abstract
A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.
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8
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Foulk MS, Urban JM, Casella C, Gerbi SA. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res 2015; 25:725-35. [PMID: 25695952 PMCID: PMC4417120 DOI: 10.1101/gr.183848.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/18/2015] [Indexed: 01/02/2023]
Abstract
Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand–independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo–controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na+ instead of K+ in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq.
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Affiliation(s)
- Michael S Foulk
- Brown University Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, Rhode Island 02912, USA
| | - John M Urban
- Brown University Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, Rhode Island 02912, USA
| | - Cinzia Casella
- Brown University Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, Rhode Island 02912, USA
| | - Susan A Gerbi
- Brown University Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, Rhode Island 02912, USA
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9
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Kovac MB, Kovacova M, Bachraty H, Bachrata K, Piscuoglio S, Hutter P, Ilencikova D, Bartosova Z, Tomlinson I, Roethlisberger B, Heinimann K. High-resolution breakpoint analysis provides evidence for the sequence-directed nature of genome rearrangements in hereditary disorders. Hum Mutat 2014; 36:250-9. [PMID: 25418510 DOI: 10.1002/humu.22734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/10/2014] [Indexed: 01/09/2023]
Abstract
Although most of the pertinent data on the sequence-directed processes leading to genome rearrangements (GRs) have come from studies on somatic tissues, little is known about GRs in the germ line of patients with hereditary disorders. This study aims at identifying DNA motifs and higher order structures of genome architecture, which can result in losses and gains of genetic material in the germ line. We first identified candidate motifs by studying 112 pathogenic germ-line GRs in hereditary colorectal cancer patients, and subsequently created an algorithm, termed recombination type ratio, which correctly predicts the propensity of rearrangements with respect to homologous versus nonhomologous recombination events.
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Affiliation(s)
- Michal B Kovac
- Research Group Human Genomics, Department of Biomedicine, University of Basel, Basel, Switzerland; Medical Genetics, University Hospital Basel, Basel, Switzerland; The Wellcome Trust Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford, UK
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10
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Angrisano T, Schiattarella GG, Keller S, Pironti G, Florio E, Magliulo F, Bottino R, Pero R, Lembo F, Avvedimento EV, Esposito G, Trimarco B, Chiariotti L, Perrino C. Epigenetic switch at atp2a2 and myh7 gene promoters in pressure overload-induced heart failure. PLoS One 2014; 9:e106024. [PMID: 25181347 PMCID: PMC4152141 DOI: 10.1371/journal.pone.0106024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/27/2014] [Indexed: 11/19/2022] Open
Abstract
Re-induction of fetal genes and/or re-expression of postnatal genes represent hallmarks of pathological cardiac remodeling, and are considered important in the progression of the normal heart towards heart failure (HF). Whether epigenetic modifications are involved in these processes is currently under investigation. Here we hypothesized that histone chromatin modifications may underlie changes in the gene expression program during pressure overload-induced HF. We evaluated chromatin marks at the promoter regions of the sarcoplasmic reticulum Ca2+ATPase (SERCA-2A) and β-myosin-heavy chain (β-MHC) genes (Atp2a2 and Myh7, respectively) in murine hearts after one or eight weeks of pressure overload induced by transverse aortic constriction (TAC). As expected, all TAC hearts displayed a significant reduction in SERCA-2A and a significant induction of β-MHC mRNA levels. Interestingly, opposite histone H3 modifications were identified in the promoter regions of these genes after TAC, including H3 dimethylation (me2) at lysine (K) 4 (H3K4me2) and K9 (H3K9me2), H3 trimethylation (me3) at K27 (H3K27me3) and dimethylation (me2) at K36 (H3K36me2). Consistently, a significant reduction of lysine-specific demethylase KDM2A could be found after eight weeks of TAC at the Atp2a2 promoter. Moreover, opposite changes in the recruitment of DNA methylation machinery components (DNA methyltransferases DNMT1 and DNMT3b, and methyl CpG binding protein 2 MeCp2) were found at the Atp2a2 or Myh7 promoters after TAC. Taken together, these results suggest that epigenetic modifications may underlie gene expression reprogramming in the adult murine heart under conditions of pressure overload, and might be involved in the progression of the normal heart towards HF.
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Affiliation(s)
- Tiziana Angrisano
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
- Department of Biology, Federico II University, Naples, Italy
| | | | - Simona Keller
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Gianluigi Pironti
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ermanno Florio
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Fabio Magliulo
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Roberta Bottino
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Raffaela Pero
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Francesca Lembo
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | | | - Giovanni Esposito
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Bruno Trimarco
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
- * E-mail: (LC); (CP)
| | - Cinzia Perrino
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
- * E-mail: (LC); (CP)
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11
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O'Sullivan JM, Hendy MD, Pichugina T, Wake GC, Langowski J. The statistical-mechanics of chromosome conformation capture. Nucleus 2013; 4:390-8. [PMID: 24051548 PMCID: PMC3899129 DOI: 10.4161/nucl.26513] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Since Jacob and Monod’s characterization of the role of DNA elements in gene control, it has been recognized that the linear organization of genome structure is important for the regulation of gene transcription and hence the manifestation of phenotypes. Similarly, it has long been hypothesized that the spatial organization (in three dimensions evolving through time), as part of the epigenome, makes a significant contribution to the genotype-phenotype transition. Proximity ligation assays commonly known as chromosome conformation capture (3C) and 3C based methodologies (e.g., GCC, HiC, and ChIA-Pet) are increasingly being incorporated into empirical studies to investigate the role that three-dimensional genome structure plays in the regulation of phenotype. The apparent simplicity of these methodologies—crosslink chromatin, digest, dilute, ligate, detect interactions—belies the complexity of the data and the considerations that should be taken into account to ensure the generation and accurate interpretation of reliable data. Here we discuss the probabilistic nature of these methodologies and how this contributes to their endogenous limitations.
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Affiliation(s)
- Justin M O'Sullivan
- Liggins Institute; University of Auckland; Auckland, New Zealand; Mathematics and Statistics; University of Otago; Dunedin, New Zealand; Institute of Natural and Mathematical Sciences; Massey University; Auckland, New Zealand; Deutsches Krebsforschungszentrum; Biophysics of Macromolecules; Heidelberg, Germany
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