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Regulation of Nuclear Mechanics and the Impact on DNA Damage

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Regulation of Nuclear Mechanics and the Impact on DNA Damage International Journal of Molecular Sciences Review Regulation of Nuclear Mechanics and the Impact on DNA Damage Ália dos Santos 1,* and Christopher P. Toseland 1,2,* 1 Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK 2 Insigneo Institute for in Silico Medicine, University of Sheffield, Sheffield S10 2RX, UK * Correspondence: a.d.santos@sheffield.ac.uk (Á.d.S.); c.toseland@sheffield.ac.uk (C.P.T.) Abstract: In eukaryotic cells, the nucleus houses the genomic material of the cell. The physical properties of the nucleus and its ability to sense external mechanical cues are tightly linked to the regulation of cellular events, such as gene expression. Nuclear mechanics and morphology are altered in many diseases such as cancer and premature ageing syndromes. Therefore, it is important to understand how different components contribute to nuclear processes, organisation and mechanics, and how they are misregulated in disease. Although, over the years, studies have focused on the nuclear lamina—a mesh of intermediate filament proteins residing between the chromatin and the nuclear membrane—there is growing evidence that chromatin structure and factors that regulate chromatin organisation are essential contributors to the physical properties of the nucleus. Here, we review the main structural components that contribute to the mechanical properties of the nucleus, with particular emphasis on chromatin structure. We also provide an example of how nuclear stiffness can both impact and be affected by cellular processes such as DNA damage and repair. Keywords: mechanics; DNA; chromatin; nucleus; lamin; cytoskeleton; DNA damage Citation: dos Santos, Á.; Toseland, C.P. Regulation of Nuclear Mechanics and the Impact on DNA Damage. Int. 1. Introduction J. Mol. Sci. 2021, 22, 3178. https:// doi.org/10.3390/ijms22063178 The nucleus houses the genetic information necessary for the activity and survival of the cell, but as we outline in this review, the nucleus is more than just a compartment to Academic Editor: house DNA. Although the nucleus is the largest and stiffest cellular organelle, it is also a Marie-Edith Chaboute highly dynamic organelle that can sense the external environment and rapidly adapt [1–3]. The nuclear envelope comprises a double membrane—the outer nuclear membrane and the Received: 25 February 2021 inner nuclear membrane—associated with various distinct transmembrane proteins, such Accepted: 18 March 2021 as nuclear pore complexes and LEM (Lap2, emerin, and Man1)-domain proteins [4]. This is Published: 20 March 2021 followed by an assembly of lamin filaments at the nuclear interior that provides structural stability to the organelle and tether chromatin to the nuclear envelope. From the outside, the Publisher’s Note: MDPI stays neutral nucleus is linked to the cytoskeleton through the Linker of Nucleoskleton and Cytoskeleton with regard to jurisdictional claims in (LINC) complex, which also binds to the nuclear lamina [5]. This nuclear connectivity published maps and institutional affil- allows external signals to modulate nuclear functions, such as transcription [6,7] and iations. DNA replication [8,9]. Moreover, it may allow communication in the opposite direction (Figure1). Within the nucleus, the DNA associates to histone cores to form nucleosomes, the building blocks of chromatin. Through epigenetic regulation, chromatin can be packaged Copyright: © 2021 by the authors. into different conformations and higher-order structures, which determine the accessibil- Licensee MDPI, Basel, Switzerland. ity [10] of DNA to replication [11,12], transcription [13,14], and repair machinery [15,16]. This article is an open access article Higher-order compact chromatin structures, known as heterochromatin, are largely inacces- distributed under the terms and sible and are usually associated with genomic regions of low transcriptional activity at the conditions of the Creative Commons nuclear periphery [17–19]. Meanwhile, more open conformations of chromatin, also known Attribution (CC BY) license (https:// as euchromatin, are easily accessible and represent areas of active gene expression [20,21]. creativecommons.org/licenses/by/ 4.0/). Int. J. Mol. Sci. 2021, 22, 3178. https://doi.org/10.3390/ijms22063178 https://www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2021, 22, x FOR Int.PEER J. Mol. REVIEW Sci. 2021 , 22, 3178 2 of 19 2 of 18 FigureFigure 1. 1. Schematic Schematic representation representation of the of interconnectivity the interconnectivity between cytoskeleton,between cytoskeleton, nuclear envelope nuclear and en- chromatin. Thevelope cytoskeleton and chromatin. is physically The connected cytoskeleton to the nuclear is physically envelope consistingconnected of theto the outer nuclear nuclear envelop membranee con- (ONM) and thesisting inner nuclearof the outer membrane nuclear (INM) membrane through the (ONM) LINC complex. and the The inner LINC nuclear complex membrane is formed of (I trimersNM) through of SUN-domain proteinsthe LINC that bindcomplex. different The KASH-domain LINC complex proteins is atformed the nuclear of trimers membrane. of SUN LINC- complexesdomain proteins can indirectly that associate bind with intermediarydifferent KASH filaments-domain and microtubules proteins throughat the nuclear cyto-linker membrane. proteins or LINC motor proteins,complexes respectively, can indirectly or directly as- interact withsociate actin filaments.with intermediary At the nuclear filaments interior, the and nuclear microtubules lamina tethers through chromatin cyto domains—lamina-associated-linker proteins or motor domains—to the nuclear envelope. This allows effective mechanotransduction in the cell. proteins, respectively, or directly interact with actin filaments. At the nuclear interior, the nu- clear lamina tethers chromatinVariations domains to the— biochemicallamina-associ componentsated domains of the—to nucleus the nuclear result inenve- changes to the lope. This allows effectivephysical mechanotransduction properties of the organelle in the and cell. its morphology. The nuclear mechanical properties, comprising the viscoelastic behaviour and plasticity, are tightly linked to cellular function Within the nucleus,and vary the between DNA cellassociates stages and to types histone [22]. Therecores are to fourform major nucleosomes, contributors tothe nuclear building blocks of chromatin.shape and the Through mechanical epigenetic properties: regulation, the magnitude chromatin of cytoskeletal can forcesbe packaged exerted on the organelle, the composition and thickness of the nuclear lamina, the level of chromatin into different conformationscompaction and within higher the nucleus,-order andstructures the activity, which of proteins determine that modulate the accessibil- DNA structure ity [10] of DNA to replication(Figure2). [11,12], transcription [13,14], and repair machinery [15,16]. Higher-order compact chromatinAltered nuclear structures, morphology known and mechanics as heterochromati are usually accompaniedn, are largely by inac- changes in cessible and are usuallygene expressionassociated and with cell function.genomic Changes regions in of the low shape transcriptional and size of the nucleus activity have at been reported for different diseases, and in some cases, this can also be used to help diagnosis. the nuclear peripheryFor [17 example,–19]. abnormallyMeanwhile, shaped more nuclei open can conformations be found in cardiomyopathies, of chromatin, progeria also and known as euchromatin,in cancer. are easily In particular, accessible nuclei and of represent cervical cancer areas cells of presentactive gene herniations expression or blebbing, [20,21]. and this constitutes part of the Pap smear test diagnosis [23]; in breast cancer, nuclear Variations to thepleomorphisms biochemical (altered components nuclear morphology) of the nucleus are used result for tumour in changes grading and to correlatesthe physical properties withof the patient organelle outcome and [24 its]. Itmorphology. is therefore essential The nuclear to understand mechanical how these proper- changes in nuclear morphology arise, how they reflect altered mechanical properties of the nucleus ties, comprising theand viscoelastic how this affects behaviour overall cellular and plasticity, function, mechanosensing are tightly linked and force to transduction. cellular function and vary betweenHere, cell we stages pay special and attention types [22] to the. There newly are emerging four datamajor on contributors the importance to of chro- nuclear shape and thematin mechanical dynamics andproperties: the regulation the magnitude of its spatial organisation.of cytoskeletal We alsoforces discuss exerted some new on the organelle, thetechnological compositio approachesn and thickness in mechanobiology of the nuclear and in lamina the study, the of chromatin level of architecture.chro- Finally, we will discuss how nuclear mechanics can influence cellular processes such as matin compaction withinDNA damage. the nucleus, and the activity of proteins that modulate DNA structure (Figure 2). Int.Int. J. J.Mol. Mol. Sci. Sci. 20212021,, 2222,, x 3178 FOR PEER REVIEW 3 of 18 3 of 19 Figure 2. Major contributors to nuclear morphology and mechanics. There are four major contribu- torsFigure to nuclear 2. Major mechanics contributors in the cell. to nuclear (i) Cytoskeletal morphology forces determine and mechanics. nuclear shapeThere and are morphology.four major contrib- Increasedutors to actinnuclear polymerisation
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