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Abstract
Physiological and pathological roles for R-loop structures continue to be discovered, and studies suggest that R-loops could contribute to human disease. R-loops are nucleic acid structures characterized by a DNA:RNA hybrid and displaced single-stranded DNA that occur in connection with transcription. R-loops form naturally and have been shown to be important for a number of physiological processes such as mitochondrial replication initiation, class switch recombination, DNA repair, modulating DNA topology, and regulation of gene expression. However, subsets of R-loops or persistent R-loops lead to DNA breaks, chromosome rearrangement, and genome instability. In addition, R-loops have been linked to human diseases, specifically neurological disorders and cancer. Of the large amount of research produced recently on R-loops, this review covers evidence for R-loop involvement in normal cellular physiology and pathophysiology, as well as describing factors that contribute to R-loop regulation.
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Affiliation(s)
- Ryan Patrick Mackay
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Qinqin Xu
- Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Paul M Weinberger
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA.,Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
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2
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Chedin F, Benham CJ. Emerging roles for R-loop structures in the management of topological stress. J Biol Chem 2020; 295:4684-4695. [PMID: 32107311 DOI: 10.1074/jbc.rev119.006364] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
R-loop structures are a prevalent class of alternative non-B DNA structures that form during transcription upon invasion of the DNA template by the nascent RNA. R-loops form universally in the genomes of organisms ranging from bacteriophages, bacteria, and yeasts to plants and animals, including mammals. A growing body of work has linked these structures to both physiological and pathological processes, in particular to genome instability. The rising interest in R-loops is placing new emphasis on understanding the fundamental physicochemical forces driving their formation and stability. Pioneering work in Escherichia coli revealed that DNA topology, in particular negative DNA superhelicity, plays a key role in driving R-loops. A clear role for DNA sequence was later uncovered. Here, we review and synthesize available evidence on the roles of DNA sequence and DNA topology in controlling R-loop formation and stability. Factoring in recent developments in R-loop modeling and single-molecule profiling, we propose a coherent model accounting for the interplay between DNA sequence and DNA topology in driving R-loop structure formation. This model reveals R-loops in a new light as powerful and reversible topological stress relievers, an insight that significantly expands the repertoire of R-loops' potential biological roles under both normal and aberrant conditions.
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Affiliation(s)
- Frederic Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616 .,Genome Center, University of California, Davis, California 95616
| | - Craig J Benham
- Genome Center, University of California, Davis, California 95616 .,Departments of Mathematics and Biomedical Engineering, University of California, Davis, California 95616
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3
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Silva-Santos AR, Alves CP, Monteiro G, Azevedo AM, Prazeres DMF. Multimodal chromatography of supercoiled minicircles: A closer look into DNA-ligand interactions. Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2018.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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4
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Imre L, Simándi Z, Horváth A, Fenyőfalvi G, Nánási P, Niaki EF, Hegedüs É, Bacsó Z, Weyemi U, Mauser R, Ausio J, Jeltsch A, Bonner W, Nagy L, Kimura H, Szabó G. Nucleosome stability measured in situ by automated quantitative imaging. Sci Rep 2017; 7:12734. [PMID: 28986581 PMCID: PMC5630628 DOI: 10.1038/s41598-017-12608-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/06/2017] [Indexed: 02/07/2023] Open
Abstract
Current approaches have limitations in providing insight into the functional properties of particular nucleosomes in their native molecular environment. Here we describe a simple and powerful method involving elution of histones using intercalators or salt, to assess stability features dependent on DNA superhelicity and relying mainly on electrostatic interactions, respectively, and measurement of the fraction of histones remaining chromatin-bound in the individual nuclei using histone type- or posttranslational modification- (PTM-) specific antibodies and automated, quantitative imaging. The method has been validated in H3K4me3 ChIP-seq experiments, by the quantitative assessment of chromatin loop relaxation required for nucleosomal destabilization, and by comparative analyses of the intercalator and salt induced release from the nucleosomes of different histones. The accuracy of the assay allowed us to observe examples of strict association between nucleosome stability and PTMs across cell types, differentiation state and throughout the cell-cycle in close to native chromatin context, and resolve ambiguities regarding the destabilizing effect of H2A.X phosphorylation. The advantages of the in situ measuring scenario are demonstrated via the marked effect of DNA nicking on histone eviction that underscores the powerful potential of topological relaxation in the epigenetic regulation of DNA accessibility.
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Affiliation(s)
- László Imre
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Zoltán Simándi
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4032, Hungary.,Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Attila Horváth
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - György Fenyőfalvi
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Péter Nánási
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Erfaneh Firouzi Niaki
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Éva Hegedüs
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Zsolt Bacsó
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Urbain Weyemi
- Center for Cancer Research National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Rebekka Mauser
- Institute of Biochemistry, Stuttgart University, Stuttgart, Germany
| | - Juan Ausio
- University of Victoria, Department of Biochemistry, Victoria, BC, V8W 3P6, Canada
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Stuttgart, Germany
| | - William Bonner
- Center for Cancer Research National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - László Nagy
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4032, Hungary.,Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA.,MTA-DE "Lendulet" Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary
| | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Gábor Szabó
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary.
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Guo P, Lam SL. The competing mini-dumbbell mechanism: new insights into CCTG repeat expansion. Signal Transduct Target Ther 2016; 1:16028. [PMID: 29263904 PMCID: PMC5661647 DOI: 10.1038/sigtrans.2016.28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 12/20/2022] Open
Abstract
CCTG repeat expansions in intron 1 of the cellular nucleic acid-binding protein gene are associated with myotonic dystrophy type 2. Recently, we have reported a novel mini-dumbbell (MDB) structure formed by two CCTG or TTTA repeats, which potentially has a critical role in repeat expansions. Here we present a mechanism, called the competing MDB mechanism, to explain how the formation of MDB can lead to efficient mismatch repair (MMR) escape and thus CCTG repeat expansions during DNA replication. In a long tract of CCTG repeats, two competing MDBs can be formed in any segment of three repeats. Fast exchange between these MDBs will make the commonly occupied repeat behave like a mini-loop. Further participations of the 5'- or 3'-flanking repeat in forming competing MDBs will make the mini-loop shift in the 5'- or 3'-direction, thereby providing a pathway for the mini-loop to escape from MMR. To avoid the complications due to the formation of hairpin conformers in longer CCTG repeats, we made use of TTTA repeats as model sequences to demonstrate the formation of competing MDBs and shifting of mini-loop in a long tract of repeating sequence.
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Affiliation(s)
- Pei Guo
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
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6
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Guo P, Lam SL. Unusual structures of CCTG repeats and their participation in repeat expansion. Biomol Concepts 2016; 7:331-340. [DOI: 10.1515/bmc-2016-0024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/01/2016] [Indexed: 11/15/2022] Open
Abstract
AbstractCCTG repeat expansion in intron 1 of the cellular nucleic acid-binding protein (CNBP) gene has been identified to be the genetic cause of myotonic dystrophy type 2 (DM2). Yet the underlying reasons for the genetic instability in CCTG repeats remain elusive. In recent years, CCTG repeats have been found to form various types of unusual secondary structures including mini-dumbbell (MDB), hairpin and dumbbell, revealing that there is a high structural diversity in CCTG repeats intrinsically. Upon strand slippage, the formation of unusual structures in the nascent strand during DNA replication has been proposed to be the culprit of CCTG repeat expansions. On the one hand, the thermodynamic stability, size, and conformational dynamics of these unusual structures affect the propensity of strand slippage. On the other hand, these structural properties determine whether the unusual structure can successfully escape from DNA repair. In this short overview, we first summarize the recent advances in elucidating the solution structures of CCTG repeats. We then discuss the potential pathways by which these unusual structures bring about variable sizes of repeat expansion, high strand slippage propensity and efficient repair escape.
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Affiliation(s)
- Pei Guo
- 1Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Sik Lok Lam
- 1Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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7
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Sutthibutpong T, Harris SA, Noy A. Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA. J Chem Theory Comput 2015; 11:2768-75. [PMID: 26575569 DOI: 10.1021/acs.jctc.5b00035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thana Sutthibutpong
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
| | - Sarah A. Harris
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
| | - Agnes Noy
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
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8
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Du X, Gertz EM, Wojtowicz D, Zhabinskaya D, Levens D, Benham CJ, Schäffer AA, Przytycka TM. Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation. Nucleic Acids Res 2014; 42:12367-79. [PMID: 25336616 PMCID: PMC4227770 DOI: 10.1093/nar/gku921] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
While individual non-B DNA structures have been shown to impact gene expression, their broad regulatory role remains elusive. We utilized genomic variants and expression quantitative trait loci (eQTL) data to analyze genome-wide variation propensities of potential non-B DNA regions and their relation to gene expression. Independent of genomic location, these regions were enriched in nucleotide variants. Our results are consistent with previously observed mutagenic properties of these regions and counter a previous study concluding that G-quadruplex regions have a reduced frequency of variants. While such mutagenicity might undermine functionality of these elements, we identified in potential non-B DNA regions a signature of negative selection. Yet, we found a depletion of eQTL-associated variants in potential non-B DNA regions, opposite to what might be expected from their proposed regulatory role. However, we also observed that genes downstream of potential non-B DNA regions showed higher expression variation between individuals. This coupling between mutagenicity and tolerance for expression variability of downstream genes may be a result of evolutionary adaptation, which allows reconciling mutagenicity of non-B DNA structures with their location in functionally important regions and their potential regulatory role.
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Affiliation(s)
- Xiangjun Du
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - E Michael Gertz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Damian Wojtowicz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Dina Zhabinskaya
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Levens
- UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Craig J Benham
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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9
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Muskhelishvili G, Travers A. Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell Mol Life Sci 2013; 70:4555-67. [PMID: 23771629 PMCID: PMC11113758 DOI: 10.1007/s00018-013-1394-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 11/29/2022]
Abstract
Understanding genetic regulation is a problem of fundamental importance. Recent studies have made it increasingly evident that, whereas the cellular genetic regulation system embodies multiple disparate elements engaged in numerous interactions, the central issue is the genuine function of the DNA molecule as information carrier. Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer. These two DNA information types are intrinsically coupled in the primary sequence organisation, and this coupling is directly relevant to regulation of the genetic function. In this review, we emphasise the critical need of holistic integration of the DNA information as a prerequisite for understanding the organisational complexity of the genetic regulation system.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany,
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10
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Levens D. Cellular MYCro economics: Balancing MYC function with MYC expression. Cold Spring Harb Perspect Med 2013; 3:3/11/a014233. [PMID: 24186489 DOI: 10.1101/cshperspect.a014233] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The expression levels of the MYC oncoprotein have long been recognized to be associated with the outputs of major cellular processes including proliferation, cell growth, apoptosis, differentiation, and metabolism. Therefore, to understand how MYC operates, it is important to define quantitatively the relationship between MYC input and expression output for its targets as well as the higher-order relationships between the expression levels of subnetwork components and the flow of information and materials through those networks. Two different views of MYC are considered, first as a molecular microeconomic manager orchestrating specific positive and negative responses at individual promoters in collaboration with other transcription and chromatin components, and second, as a macroeconomic czar imposing an overarching rule onto all active genes. In either case, c-myc promoter output requires multiple inputs and exploits diverse mechanisms to tune expression to the appropriate levels relative to the thresholds of expression that separate health and disease.
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Affiliation(s)
- David Levens
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-1500
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11
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Abstract
How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.
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12
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Du X, Wojtowicz D, Bowers AA, Levens D, Benham CJ, Przytycka TM. The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli. Nucleic Acids Res 2013; 41:5965-77. [PMID: 23620297 PMCID: PMC3695496 DOI: 10.1093/nar/gkt308] [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] [Indexed: 11/14/2022] Open
Abstract
Although the right-handed double helical B-form DNA is most common under physiological conditions, DNA is dynamic and can adopt a number of alternative structures, such as the four-stranded G-quadruplex, left-handed Z-DNA, cruciform and others. Active transcription necessitates strand separation and can induce such non-canonical forms at susceptible genomic sequences. Therefore, it has been speculated that these non-B DNA motifs can play regulatory roles in gene transcription. Such conjecture has been supported in higher eukaryotes by direct studies of several individual genes, as well as a number of large-scale analyses. However, the role of non-B DNA structures in many lower organisms, in particular proteobacteria, remains poorly understood and incompletely documented. In this study, we performed the first comprehensive study of the occurrence of B DNA-non-B DNA transition-susceptible sites (non-B DNA motifs) within the context of the operon structure of the Escherichia coli genome. We compared the distributions of non-B DNA motifs in the regulatory regions of operons with those from internal regions. We found an enrichment of some non-B DNA motifs in regulatory regions, and we show that this enrichment cannot be simply explained by base composition bias in these regions. We also showed that the distribution of several non-B DNA motifs within intergenic regions separating divergently oriented operons differs from the distribution found between convergent ones. In particular, we found a strong enrichment of cruciforms in the termination region of operons; this enrichment was observed for operons with Rho-dependent, as well as Rho-independent terminators. Finally, a preference for some non-B DNA motifs was observed near transcription factor-binding sites. Overall, the conspicuous enrichment of transition-susceptible sites in these specific regulatory regions suggests that non-B DNA structures may have roles in the transcriptional regulation of specific operons within the E. coli genome.
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Affiliation(s)
- Xiangjun Du
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bethesda, MD 20894, USA
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13
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Mitchell JS, Harris SA. Thermodynamics of writhe in DNA minicircles from molecular dynamics simulations. PHYSICAL REVIEW LETTERS 2013; 110:148105. [PMID: 25167042 DOI: 10.1103/physrevlett.110.148105] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Indexed: 06/03/2023]
Abstract
DNA supercoiling plays a role in genetic control by imposing torsional stress. This can induce writhe, which changes the global shape of the DNA. We have used atomistic molecular dynamics simulations to partition the free energy changes driving the writhing and unwrithing transitions in supercoiled minicircle DNA. The calculations show that while writhing is energetically driven, the unwrithing transition occurs because the circular state has a higher configurational entropy than the plectoneme. Writhing improves the van der Waals interactions between stacked bases, but can be suppressed by electrostatic repulsion within the negatively charged backbone strands in low salt conditions where electrostatic screening is poor. The free energy difference between circular and plectonemic DNA is determined by such a delicate balance of opposing thermodynamic terms that any perturbation in the environment, such as a change in salt concentration, can be sufficient to convert between these two states. This switchable behavior provides a mechanism for supercoiled DNA to store and communicate biological information physically as well as chemically.
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Affiliation(s)
- Jonathan S Mitchell
- Section de Mathematiques, Ecole Polytechnique Federale de Lausanne, Lausanne 1015, Switzerland
| | - Sarah A Harris
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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14
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Sobetzko P, Glinkowska M, Travers A, Muskhelishvili G. DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle. MOLECULAR BIOSYSTEMS 2013; 9:1643-51. [PMID: 23493878 DOI: 10.1039/c3mb25515h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The chromosomal DNA polymer constituting the cellular genetic material is primarily a device for coding information. Whilst the gene sequences comprise the digital (discontinuous) linear code, physiological alterations of the DNA superhelical density generate in addition analog (continuous) three-dimensional information essential for regulation of both chromosome compaction and gene expression. Insight into the relationship between the DNA analog information and the digital linear code is of fundamental importance for understanding genetic regulation. Our previous study in the model organism Escherichia coli suggested that the chromosomal gene order and a spatiotemporal gradient of DNA superhelicity associated with DNA replication determine the growth phase-dependent gene transcription. In this study we reveal a general gradient of DNA thermodynamic stability correlated with the polarity of chromosomal replication and manifest in the spatiotemporal pattern of gene transcription during the bacterial growth cycle. Furthermore, by integrating the physical and dynamic features of the transcribed sequences with their functional content we identify spatiotemporal domains of gene expression encompassing different functions. We thus provide both an insight into the organisational principle of the bacterial growth program and a novel holistic methodology for exploring chromosomal dynamics.
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Affiliation(s)
- Patrick Sobetzko
- Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, D-28759 Bremen, Germany
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15
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Potoyan DA, Savelyev A, Papoian GA. Recent successes in coarse-grained modeling of DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1114] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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16
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Lesne A, Bécavin C, Victor JM. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing. Phys Biol 2012; 9:013001. [PMID: 22314931 DOI: 10.1088/1478-3975/9/1/013001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.
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Affiliation(s)
- Annick Lesne
- CNRS UMR 7600, Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France.
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