Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners

Local volume concentration, packing domains, and scaling properties of chromatin

We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally defined domains observed by single-cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as RAD21 degradation.

Vertebrate centromere architecture: from chromatin threads to functional structures

Centromeres are chromatin structures specialized in sister chromatid cohesion, kinetochore assembly, and microtubule attachment during chromosome segregation. The regional centromere of vertebrates consists of long regions of highly repetitive sequences occupied by the Histone H3 variant CENP-A, and which are flanked by pericentromeres. The three-dimensional organization of centromeric chromatin is paramount for its functionality and its ability to withstand spindle forces. Alongside CENP-A, key contributors to the folding of this structure include components of the Constitutive Centromere-Associated Network (CCAN), the protein CENP-B, and condensin and cohesin complexes. Despite its importance, the intricate architecture of the regional centromere of vertebrates remains largely unknown. Recent advancements in long-read sequencing, super-resolution and cryo-electron microscopy, and chromosome conformation capture techniques have significantly improved our understanding of this structure at various levels, from the linear arrangement of centromeric sequences and their epigenetic landscape to their higher-order compaction. In this review, we discuss the latest insights on centromere organization and place them in the context of recent findings describing a bipartite higher-order organization of the centromere.

Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin

We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally-defined domains observed by single cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as Rad21 degradation.

Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin

Centromeres are scaffolds for the assembly of kinetochores that ensure chromosome segregation during cell division. How vertebrate centromeres obtain a three-dimensional structure to accomplish their primary function is unclear. Using super-resolution imaging, capture-C, and polymer modeling, we show that vertebrate centromeres are partitioned by condensins into two subdomains during mitosis. The bipartite structure is found in human, mouse, and chicken cells and is therefore a fundamental feature of vertebrate centromeres. Super-resolution imaging and electron tomography reveal that bipartite centromeres assemble bipartite kinetochores, with each subdomain binding a distinct microtubule bundle. Cohesin links the centromere subdomains, limiting their separation in response to spindle forces and avoiding merotelic kinetochore-spindle attachments. Lagging chromosomes during cancer cell divisions frequently have merotelic attachments in which the centromere subdomains are separated and bioriented. Our work reveals a fundamental aspect of vertebrate centromere biology with implications for understanding the mechanisms that guarantee faithful chromosome segregation.

Native and tagged CENP-A histones are functionally inequivalent

BACKGROUND

Over the past several decades, the use of biochemical and fluorescent tags has elucidated mechanistic and cytological processes that would otherwise be impossible. The challenging nature of certain nuclear proteins includes low abundancy, poor antibody recognition, and transient dynamics. One approach to get around those issues is the addition of a peptide or larger protein tag to the target protein to improve enrichment, purification, and visualization. However, many of these studies were done under the assumption that tagged proteins can fully recapitulate native protein function.

RESULTS

We report that when C-terminally TAP-tagged CENP-A histone variant is introduced, it undergoes altered kinetochore protein binding, differs in post-translational modifications (PTMs), utilizes histone chaperones that differ from that of native CENP-A, and can partially displace native CENP-A in human cells. Additionally, these tagged CENP-A-containing nucleosomes have reduced centromeric incorporation at early G1 phase and poorly associates with linker histone H1.5 compared to native CENP-A nucleosomes.

CONCLUSIONS

These data suggest expressing tagged versions of histone variant CENP-A may result in unexpected utilization of non-native pathways, thereby altering the biological function of the histone variant.

Actin contraction controls nuclear blebbing and rupture independent of actin confinement

The nucleus is a mechanically stable compartment of the cell that contains the genome and performs many essential functions. Nuclear mechanical components chromatin and lamins maintain nuclear shape, compartmentalization, and function by resisting antagonistic actin contraction and confinement. Studies have yet to compare chromatin and lamins perturbations side-by-side as well as modulated actin contraction while holding confinement constant. To accomplish this, we used nuclear localization signal green fluorescent protein to measure nuclear shape and rupture in live cells with chromatin and lamin perturbations. We then modulated actin contraction while maintaining actin confinement measured by nuclear height. Wild type, chromatin decompaction, and lamin B1 null present bleb-based nuclear deformations and ruptures dependent on actin contraction and independent of actin confinement. Actin contraction inhibition by Y27632 decreased nuclear blebbing and ruptures while activation by CN03 increased rupture frequency. Lamin A/C null results in overall abnormal shape also reliant on actin contraction, but similar blebs and ruptures as wild type. Increased DNA damage is caused by nuclear blebbing or abnormal shape which can be relieved by inhibition of actin contraction which rescues nuclear shape and decreases DNA damage levels in all perturbations. Thus, actin contraction drives nuclear blebbing, bleb-based ruptures, and abnormal shape independent of changes in actin confinement.

Extracellular Matrix Cues Regulate Mechanosensing and Mechanotransduction of Cancer Cells

Extracellular biophysical properties have particular implications for a wide spectrum of cellular behaviors and functions, including growth, motility, differentiation, apoptosis, gene expression, cell-matrix and cell-cell adhesion, and signal transduction including mechanotransduction. Cells not only react to unambiguously mechanical cues from the extracellular matrix (ECM), but can occasionally manipulate the mechanical features of the matrix in parallel with biological characteristics, thus interfering with downstream matrix-based cues in both physiological and pathological processes. Bidirectional interactions between cells and (bio)materials in vitro can alter cell phenotype and mechanotransduction, as well as ECM structure, intentionally or unintentionally. Interactions between cell and matrix mechanics in vivo are of particular importance in a variety of diseases, including primarily cancer. Stiffness values between normal and cancerous tissue can range between 500 Pa (soft) and 48 kPa (stiff), respectively. Even the shear flow can increase from 0.1-1 dyn/cm2 (normal tissue) to 1-10 dyn/cm2 (cancerous tissue). There are currently many new areas of activity in tumor research on various biological length scales, which are highlighted in this review. Moreover, the complexity of interactions between ECM and cancer cells is reduced to common features of different tumors and the characteristics are highlighted to identify the main pathways of interaction. This all contributes to the standardization of mechanotransduction models and approaches, which, ultimately, increases the understanding of the complex interaction. Finally, both the in vitro and in vivo effects of this mechanics-biology pairing have key insights and implications for clinical practice in tumor treatment and, consequently, clinical translation.

The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea

Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.

CENP-A and CENP-B collaborate to create an open centromeric chromatin state

Centromeres are epigenetically defined via the presence of the histone H3 variant CENP-A. Contacting CENP-A nucleosomes, the constitutive centromere associated network (CCAN) and the kinetochore assemble, connecting the centromere to spindle microtubules during cell division. The DNA-binding centromeric protein CENP-B is involved in maintaining centromere stability and, together with CENP-A, shapes the centromeric chromatin state. The nanoscale organization of centromeric chromatin is not well understood. Here, we use single-molecule fluorescence and cryoelectron microscopy (cryoEM) to show that CENP-A incorporation establishes a dynamic and open chromatin state. The increased dynamics of CENP-A chromatin create an opening for CENP-B DNA access. In turn, bound CENP-B further opens the chromatin fiber structure and induces nucleosomal DNA unwrapping. Finally, removal of CENP-A increases CENP-B mobility in cells. Together, our studies show that the two centromere-specific proteins collaborate to reshape chromatin structure, enabling the binding of centromeric factors and establishing a centromeric chromatin state.

Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin

We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions that is able to capture the observed behavior across imaging and sequencing based measures of chromatin organization. The SR-EV model takes the return rules of the Self Returning Random Walk, incorporates excluded volume interactions, chain connectivity and expands the length scales range from 10 nm to over 1 micron. The model is computationally fast and we created thousands of configurations that we grouped in twelve different ensembles according to the two main parameters of the model. The analysis of the configurations was done in a way completely analogous to the experimental treatments used to determine chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. We find a robust agreement between the theoretical and experimental results. The overall organization of the model chromatin is corrugated, with dense packing domains alternating with a very dilute regions in a manner that resembles the mixing of two disordered bi-continuous phases. The return rules combined with excluded volume interactions lead to the formation of packing domains. We observed a transition from a short scale regime to a long scale regime occurring at genomic separations of ~ 4 × 104 base pairs or ~ 100 nm in distance. The contact probability reflects this transition with a change in the scaling exponent from larger than -1 to approximately -1. The analysis of the pair correlation function reveals that chromatin organizes following a power law scaling with exponent D ∈ { 2 , 3 } in the transition region between the short and long distance regimes.

Single molecule analysis of CENP-A chromatin by high-speed atomic force microscopy

Chromatin accessibility is modulated in a variety of ways to create open and closed chromatin states, both of which are critical for eukaryotic gene regulation. At the single molecule level, how accessibility is regulated of the chromatin fiber composed of canonical or variant nucleosomes is a fundamental question in the field. Here, we developed a single-molecule tracking method where we could analyze thousands of canonical H3 and centromeric variant nucleosomes imaged by high-speed atomic force microscopy. This approach allowed us to investigate how changes in nucleosome dynamics in vitro inform us about transcriptional potential in vivo. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and determined the mean square displacement and diffusion constant for the variant centromeric CENP-A nucleosome. Furthermore, we found that an essential kinetochore protein CENP-C reduces the diffusion constant and mobility of centromeric nucleosomes along the chromatin fiber. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamics in vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. From these data, we speculate that factors altering nucleosome mobility in vitro, also correspondingly alter transcription in vivo. Subsequently, we propose a model in which variant nucleosomes encode their own diffusion kinetics and mobility, and where binding partners can suppress or enhance nucleosome mobility.

The Force is Strong with This Epigenome: Chromatin Structure and Mechanobiology

All life forms sense and respond to mechanical stimuli. Throughout evolution, organisms develop diverse mechanosensing and mechanotransduction pathways, leading to fast and sustained mechanoresponses. Memory and plasticity characteristics of mechanoresponses are thought to be stored in the form of epigenetic modifications, including chromatin structure alterations. These mechanoresponses in the chromatin context share conserved principles across species, such as lateral inhibition during organogenesis and development. However, it remains unclear how mechanotransduction mechanisms alter chromatin structure for specific cellular functions, and if altered chromatin structure can mechanically affect the environment. In this review, we discuss how chromatin structure is altered by environmental forces via an outside-in pathway for cellular functions, and the emerging concept of how chromatin structure alterations can mechanically affect nuclear, cellular, and extracellular environments. This bidirectional mechanical feedback between chromatin of the cell and the environment can potentially have important physiological implications, such as in centromeric chromatin regulation of mechanobiology in mitosis, or in tumor-stroma interactions. Finally, we highlight the current challenges and open questions in the field and provide perspectives for future research.

Are extraordinary nucleosome structures more ordinary than we thought?

The nucleosome is a DNA-protein assembly that is the basic unit of chromatin. A nucleosome can adopt various structures. In the canonical nucleosome structure, 145-147 bp of DNA is wrapped around a histone heterooctamer. The strong histone-DNA interactions cause the DNA to be inaccessible for nuclear processes such as transcription. Therefore, the canonical nucleosome structure has to be altered into different, non-canonical structures to increase DNA accessibility. While it is recognised that non-canonical structures do exist, these structures are not well understood. In this review, we discuss both the evidence for various non-canonical nucleosome structures in the nucleus and the factors that are believed to induce these structures. The wide range of non-canonical structures is likely to regulate the amount of accessible DNA, and thus have important nuclear functions.

Direct observation of surface charge and stiffness of human metaphase chromosomes

Metaphase chromosomes in which both polynucleotides and proteins are condensed with hierarchies are closely related to life phenomena such as cell division, cancer development, and cellular senescence. Nevertheless, their nature is rarely revealed, owing to their structural complexity and technical limitations in analytical methods. In this study, we used surface potential and nanomechanics mapping technology based on atomic force microscopy to measure the surface charge and intrinsic stiffness of metaphase chromosomes. We found that extra materials covering the chromosomes after the extraction process were positively charged. With the covering materials, the chromosomes were positively charged (ca. 44.9 ± 16.48 mV) and showed uniform stiffness (ca. 6.23 ± 1.98 MPa). In contrast, after getting rid of the extra materials through treatment with RNase and protease, the chromosomes were strongly negatively charged (ca. -197.4 ± 77.87 mV) and showed relatively non-uniform and augmented stiffness (ca. 36.87 ± 17.56 MPa). The results suggested undulating but compact coordination of condensed chromosomes. Additionally, excessive treatment with RNase and protease could destroy the chromosomal structure, providing an exceptional opportunity for multiscale stiffness mapping of polynucleotides, nucleosomes, chromatin fibers, and chromosomes in a single image. Our approach offers a new horizon in terms of an analytical technique for studying chromosome-related diseases.

Molecular dynamics simulations for the study of chromatin biology

The organization of Eukaryotic DNA into chromatin has profound implications for the processing of genetic information. In the past years, molecular dynamics (MD) simulations proved to be a powerful tool to investigate the mechanistic basis of chromatin biology. We review recent all-atom and coarse-grained MD studies revealing how the structure and dynamics of chromatin underlie its biological functions. We describe the latest method developments; the structural fluctuations of nucleosomes and the various factors affecting them; the organization of chromatin fibers, with particular emphasis on its liquid-like character; the interactions and dynamics of transcription factors on chromatin; and how chromatin organization is modulated by molecular motors acting on DNA.

Centromere Chromatin Dynamics at a Glance

The centromere is a specialized DNA locus that ensures the faithful segregation of chromosomes during cell division. It does so by directing the assembly of an essential proteinaceous structure called the kinetochore. The centromere identity is primarily epigenetically defined by a nucleosome containing an H3 variant called CENP-A as well as by the interplay of several factors such as differential chromatin organization driven by CENP-A and H2A.Z, centromere-associated proteins, and post-translational modifications. At the centromere, CENP-A is not just a driving force for kinetochore assembly but also modifies the structural and dynamic properties of the centromeric chromatin, resulting in a distinctive chromatin organization. An additional level of regulation of the centromeric chromatin conformation is provided by post-translational modifications of the histones in the CENP-A nucleosomes. Further, H2A.Z is present in the regions flanking the centromere for heterochromatinization. In this review, we focus on the above-mentioned factors to describe how they contribute to the organization of the centromeric chromatin: CENP-A at the core centromere, post-translational modifications that decorate CENP-A, and the variant H2A.Z.

GRANT Motif Regulates CENP-A Incorporation and Restricts RNA Polymerase II Accessibility at Centromere

Precise chromosome segregation is essential for maintaining genomic stability, and its proper execution centers on the centromere, a chromosomal locus that mounts the kinetochore complex to mediate attachment of chromosomes to the spindle microtubules. The location of the centromere is epigenetically determined by a centromere-specific histone H3 variant, CENP-A. Many human cancers exhibit overexpression of CENP-A, which correlates with occurrence of aneuploidy in these malignancies. Centromeric targeting of CENP-A depends on its histone fold, but recent studies showed that the N-terminal tail domain (NTD) also plays essential roles. Here, we investigated implications of NTD in conferring aneuploidy formation when CENP-A is overexpressed in fission yeast. A series of mutant genes progressively lacking one amino acid of the NTD have been constructed for overexpression in wild-type cells using the intermediate strength nmt41 promoter. Constructs hosting disrupted GRANT (Genomic stability-Regulating site within CENP-A N-Terminus) motif in NTD results in growth retardation, aneuploidy, increased localization to the centromere, upregulated RNA polymerase II accessibility and transcriptional derepression of the repressive centromeric chromatin, suggesting that GRANT residues fine-tune centromeric CENP-A incorporation and restrict RNA polymerase II accessibility. This work highlighted the importance of CENP-A NTD, particularly the GRANT motif, in aneuploidy formation of overexpressed CENP-A in fission yeast.

Breaking the aging epigenetic barrier

Aging is an inexorable event occurring universally for all organisms characterized by the progressive loss of cell function. However, less is known about the key events occurring inside the nucleus in the process of aging. The advent of chromosome capture techniques and extensive modern sequencing technologies have illuminated a rather dynamic structure of chromatin inside the nucleus. As cells advance along their life cycle, chromatin condensation states alter which leads to a different epigenetic landscape, correlated with modified gene expression. The exact factors mediating these changes in the chromatin structure and function remain elusive in the context of aging cells. The accumulation of DNA damage, reactive oxygen species and loss of genomic integrity as cells cease to divide can contribute to a tumor stimulating environment. In this review, we focus on genomic and epigenomic changes occurring in an aged cell which can contribute to age-related tumor formation.

Tuning Formation of Protein-DNA Coacervates by Sequence and Environment

The high concentration of nucleic acids and positively charged proteins in the cell nucleus provides many possibilities for complex coacervation. We consider a prototypical mixture of nucleic acids together with the polycationic C-terminus of histone H1 (CH1). Using a minimal coarse-grained model that captures the shape, flexibility, and charge distributions of the molecules, we find that coacervates are readily formed at physiological ionic strengths, in agreement with experiment, with a progressive increase in local ordering at low ionic strength. Variation of the positions of charged residues in the protein tunes phase separation: for well-mixed or only moderately blocky distributions of charge, there is a modest increase of local ordering with increasing blockiness that is also associated with an increased propensity to phase separate. This ordering is also associated with a slowdown of rotational and translational diffusion in the dense phase. However, for more extreme blockiness (and consequently higher local charge density), we see a qualitative change in the condensed phase to become a segregated structure with a dramatically increased ordering of the DNA. Naturally occurring proteins with these sequence properties, such as protamines in sperm cells, are found to be associated with very dense packing of nucleic acids.

CENP-B-mediated DNA loops regulate activity and stability of human centromeres

Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.

Diverse mechanisms of centromere specification

The centromere performs a universally conserved function, to accurately partition genetic information upon cell division. Yet, centromeres are among the most rapidly evolving regions of the genome and are bound by a varying assortment of centromere-binding factors that are themselves highly divergent at the protein-sequence level. A common thread in most species is the dependence on the centromere-specific histone variant CENP-A for the specification of the centromere site. However, CENP-A is not universally required in all species or cell types, making the identification of a general mechanism for centromere specification challenging. In this review, we examine our current understanding of the mechanisms of centromere specification in CENP-A-dependent and independent systems, focusing primarily on recent work.

Multiscale modeling of genome organization with maximum entropy optimization

Three-dimensional (3D) organization of the human genome plays an essential role in all DNA-templated processes, including gene transcription, gene regulation, and DNA replication. Computational modeling can be an effective way of building high-resolution genome structures and improving our understanding of these molecular processes. However, it faces significant challenges as the human genome consists of over 6 × 109 base pairs, a system size that exceeds the capacity of traditional modeling approaches. In this perspective, we review the progress that has been made in modeling the human genome. Coarse-grained models parameterized to reproduce experimental data via the maximum entropy optimization algorithm serve as effective means to study genome organization at various length scales. They have provided insight into the principles of whole-genome organization and enabled de novo predictions of chromosome structures from epigenetic modifications. Applications of these models at a near-atomistic resolution further revealed physicochemical interactions that drive the phase separation of disordered proteins and dictate chromatin stability in situ. We conclude with an outlook on the opportunities and challenges in studying chromosome dynamics.

Histone tails cooperate to control the breathing of genomic nucleosomes

Genomic DNA is packaged in chromatin, a dynamic fiber variable in size and compaction. In chromatin, repeating nucleosome units wrap 145–147 DNA basepairs around histone proteins. Genetic and epigenetic regulation of genes relies on structural transitions in chromatin which are driven by intra- and inter-nucleosome dynamics and modulated by chemical modifications of the unstructured terminal tails of histones. Here we demonstrate how the interplay between histone H3 and H2A tails control ample nucleosome breathing motions. We monitored large openings of two genomic nucleosomes, and only moderate breathing of an engineered nucleosome in atomistic molecular simulations amounting to 24 μs. Transitions between open and closed nucleosome conformations were mediated by the displacement and changes in compaction of the two histone tails. These motions involved changes in the DNA interaction profiles of clusters of epigenetic regulatory aminoacids in the tails. Removing the histone tails resulted in a large increase of the amplitude of nucleosome breathing but did not change the sequence dependent pattern of the motions. Histone tail modulated nucleosome breathing is a key mechanism of chromatin dynamics with important implications for epigenetic regulation.

In the cell, the DNA is packed in chromatin. Chromatin is a highly dynamic fiber structure made of arrays of nucleosomes with different degrees of compaction. Each nucleosome has 145–147 basepairs of DNA wrapped around a protein octamer made of four unique histone proteins. Each histone is present twice and has a structured part and one or two disordered terminal tails. The regulation of gene expression in the cell and during cellular transitions depends on dynamic changes in chromatin structure. Chromatin dynamics are modulated by intra and inter nucleosome motions and by posttranslational chemical modifications of the histone tails. Here we reveal how histone tails control the intra nucleosome dynamics at atomic resolution. From extensive sampling of nucleosome dynamics in atomistic molecular simulations, we show that genomic nucleosomes breath more extensively than engineered ones and we describe how two histone tails cooperate to control nucleosome breathing through interactions between clusters of positively charged residues and the DNA. Nucleosome conformations with different degrees of opening are associated with different conformations, positions, and DNA interaction patterns of the tails. With this mechanism, we contribute to the understanding of chromatin dynamics at atomic resolution.

Mechanical properties of nucleoprotein complexes determined by nanoindentation spectroscopy

The interplay between transcription factors, chromatin remodelers, 3-D organization, and mechanical properties of the chromatin fiber controls genome function in eukaryotes. Besides the canonical histones which fold the bulk of the chromatin into nucleosomes, histone variants create distinctive chromatin domains that are thought to regulate transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether histone variants translate distinctive biochemical or biophysical properties to their associated chromatin structures, and whether these properties impact chromatin dynamics as the genome undergoes a multitude of transactions, is an important question in biology. Here, we describe single-molecule nanoindentation tools that we developed specifically to determine the mechanical properties of histone variant nucleosomes and their complexes. These methods join an array of cutting-edge new methods that further our quantitative understanding of the response of chromatin to intrinsic and extrinsic forces which act upon it during biological transactions in the nucleus.

The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity?

The centromere is an essential chromatin domain required for kinetochore recruitment and chromosome segregation in eukaryotes. To perform this role, centro-chromatin adopts a unique structure that provides access to kinetochore proteins and maintains stability under tension during mitosis. This is achieved by the presence of nucleosomes containing the H3 variant CENP-A, which also acts as the epigenetic mark defining the centromere. In this review, we discuss the role of CENP-A on the structure and dynamics of centromeric chromatin. We further discuss the impact of the CENP-A binding proteins CENP-C, CENP-N, and CENP-B on modulating centro-chromatin structure. Based on these findings we provide an overview of the higher order structure of the centromere.

DNA mechanics and its biological impact

Almost all nucleoprotein interactions and DNA manipulation events involve mechanical deformations of DNA. Extraordinary progresses in single-molecule, structural, and computational methods have characterized the average mechanical properties of DNA, such as bendability and torsional rigidity, in high resolution. Further, the advent of sequencing technology has permitted measuring, in high-throughput, how such mechanical properties vary with sequence and epigenetic modifications along genomes. We review these recent technological advancements, and discuss how they have contributed to the emerging idea that variations in the mechanical properties of DNA play a fundamental role in regulating, genome-wide, diverse processes involved in chromatin organization.

High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes

Nucleosomes, the fundamental units of chromatin, regulate readout and expression of eukaryotic genomes. Single-molecule experiments have revealed force-induced nucleosome accessibility, but a high-resolution unwrapping landscape in the absence of external forces is currently lacking. Here, we introduce a high-throughput pipeline for the analysis of nucleosome conformations based on atomic force microscopy and automated, multi-parameter image analysis. Our data set of ∼10 000 nucleosomes reveals multiple unwrapping states corresponding to steps of 5 bp DNA. For canonical H3 nucleosomes, we observe that dissociation from one side impedes unwrapping from the other side, but in contrast to force-induced unwrapping, we find only a weak sequence-dependent asymmetry. Notably, centromeric CENP-A nucleosomes do not unwrap anti-cooperatively, in stark contrast to H3 nucleosomes. Finally, our results reconcile previous conflicting findings about the differences in height between H3 and CENP-A nucleosomes. We expect our approach to enable critical insights into epigenetic regulation of nucleosome structure and stability and to facilitate future high-throughput AFM studies that involve heterogeneous nucleoprotein complexes.

CENP-A nucleosome-a chromatin-embedded pedestal for the centromere: lessons learned from structural biology

The centromere is a chromosome locus that directs equal segregation of chromosomes during cell division. A nucleosome containing the histone H3 variant CENP-A epigenetically defines the centromere. Here, we summarize findings from recent structural biology studies, including several CryoEM structures, that contributed to elucidate specific features of the CENP-A nucleosome and molecular determinants of its interactions with CENP-C and CENP-N, the only two centromere proteins that directly bind to it. Based on those findings, we propose a role of the CENP-A nucleosome in the organization of centromeric chromatin beyond binding centromeric proteins.

A histone H4 gene prevents drought-induced bolting in Chinese cabbage by attenuating the expression of flowering genes

Flowering is an important trait in Chinese cabbage, because premature flowering reduces yield and quality of the harvested products. Water deficit, caused by drought or other environmental conditions, induces early flowering. Drought resistance involves global reprogramming of transcription, hormone signaling, and chromatin modification. We show that a histone H4 protein, BrHIS4.A04, physically interacts with a homeodomain protein BrVIN3.1, which was selected during the domestication of late-bolting Chinese cabbage. Over-expression of BrHIS4.A04 resulted in premature flowering under normal growth conditions, but prevented further premature bolting in response to drought. We show that the expression of key abscisic acid (ABA) signaling genes, and also photoperiodic flowering genes was attenuated in BrHIS4.A04-overexpressing (BrHIS4.A04OE) plants under drought conditions. Furthermore, the relative change in H4-acetylation at these gene loci was reduced in BrHIS4.A04OE plants. We suggest that BrHIS4.A04 prevents premature bolting by attenuating the expression of photoperiodic flowering genes under drought conditions, through the ABA signaling pathway. Since BrHIS4.A04OE plants displayed no phenotype related to vegetative or reproductive development under laboratory-induced drought conditions, our findings contribute to the potential fine-tuning of flowering time in crops through genetic engineering without any growth penalty, although more data are necessary under field drought conditions.

CENP-A Nucleosome is a Sensitive Allosteric Scaffold for DNA and Chromatin Factors

Centromeric loci of chromosomes are defined by nucleosomes containing the histone H3 variant CENP-A, which bind their DNA termini more permissively than their canonical counterpart, a feature that is critical for the mitotic fidelity. A recent cryo-EM study demonstrated that the DNA termini of CENP-A nucleosomes, reconstituted with the Widom 601 DNA sequence, are asymmetrically flexible, meaning one terminus is more clearly resolved than the other. However, an earlier work claimed that both ends could be resolved in the presence of two stabilizing single chain variable fragment (scFv) antibodies per nucleosome, and thus are likely permanently bound to the histone octamer. This suggests that the binding of scFv antibodies to the histone octamer surface would be associated with CENP-A nucleosome conformational changes, including stable binding of the DNA termini. Here, we present computational evidence that allows to explain at atomistic level the structural rearrangements of CENP-A nucleosomes resulting from the antibody binding. The antibodies, while they only bind the octamer façades, are capable of altering the dynamics of the nucleosomal core, and indirectly also the surrounding DNA. This effect has more drastic implications for the structure and the dynamics of the CENP-A nucleosome in comparison to its canonical counterpart. Furthermore, we find evidence that the antibodies bind the left and the right octamer façades at different affinities, another manifestation of the DNA sequence. We speculate that the cells could use induction of similar allosteric effects to control centromere function.

DNA damage alters nuclear mechanics through chromatin reorganization

DNA double-strand breaks drive genomic instability. However, it remains unknown how these processes may affect the biomechanical properties of the nucleus and what role nuclear mechanics play in DNA damage and repair efficiency. Here, we have used Atomic Force Microscopy to investigate nuclear mechanical changes, arising from externally induced DNA damage. We found that nuclear stiffness is significantly reduced after cisplatin treatment, as a consequence of DNA damage signalling. This softening was linked to global chromatin decondensation, which improves molecular diffusion within the organelle. We propose that this can increase recruitment for repair factors. Interestingly, we also found that reduction of nuclear tension, through cytoskeletal relaxation, has a protective role to the cell and reduces accumulation of DNA damage. Overall, these changes protect against further genomic instability and promote DNA repair. We propose that these processes may underpin the development of drug resistance.

Breaths, Twists, and Turns of Atomistic Nucleosomes

Gene regulation programs establish cellular identity and rely on dynamic changes in the structural packaging of genomic DNA. The DNA is packaged in chromatin, which is formed from arrays of nucleosomes displaying different degree of compaction and different lengths of inter-nucleosomal linker DNA. The nucleosome represents the repetitive unit of chromatin and is formed by wrapping 145-147 basepairs of DNA around an octamer of histone proteins. Each of the four histones is present twice and has a structured core and intrinsically disordered terminal tails. Chromatin dynamics are triggered by inter- and intra-nucleosome motions that are controlled by the DNA sequence, the interactions between the histone core and the DNA, and the conformations, positions, and DNA interactions of the histone tails. Understanding chromatin dynamics requires studying all these features at the highest possible resolution. For this, molecular dynamics simulations can be used as a powerful complement or alternative to experimental approaches, from which it is often very challenging to characterize the structural features and atomic interactions controlling nucleosome motions. Molecular dynamics simulations can be performed at different resolutions, by coarse graining the molecular system with varying levels of details. Here we review the successes and the remaining challenges of the application of atomic resolution simulations to study the structure and dynamics of nucleosomes and their complexes with interacting partners.

Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin

Chromatin is the epigenomic platform for diverse nuclear processes such as DNA repair, replication, transcription, telomere, and centromere function. In cancer cells, mutations in key processes result in DNA amplification, chromosome translocations, and chromothripsis, severely distorting the natural chromatin state. In normal and diseased states, dozens of chromatin effectors alter the physical integrity and dynamics of chromatin at the level of both single nucleosomes and arrays of nucleosomes folded into 3-dimensional shapes. Integrating these length scales, from the 10 nm sized nucleosome to mitotic chromosomes, whilst jostling within the crowded environment of the cell, cannot yet be achieved by a single technology. In this review, we discuss tools that have proven powerful in the investigation of nucleosome and chromatin fiber dynamics. We also provide a deeper focus into atomic force microscopy (AFM) applications that can bridge diverse length and time scales. Using time course AFM, we observe that chromatin condensation by H1.5 is dynamic, whereas using nano-indentation force spectroscopy we observe that both histone variants and nucleosome binding partners alter material properties of individual nucleosomes. Finally, we demonstrate how high-speed AFM can visualize plasmid DNA dynamics, intermittent nucleosome-nucleosome contacts, and changes in nucleosome phasing along a contiguous chromatin fiber. Altogether, the development of innovative technologies holds the promise of revealing the secret lives of nucleosomes, potentially bridging the gaps in our understanding of how chromatin works within living cells and tissues.

Centromeric Transcription: A Conserved Swiss-Army Knife

In most species, the centromere is comprised of repetitive DNA sequences, which rapidly evolve. Paradoxically, centromeres fulfill an essential function during mitosis, as they are the chromosomal sites wherein, through the kinetochore, the mitotic spindles bind. It is now generally accepted that centromeres are transcribed, and that such transcription is associated with a broad range of functions. More than a decade of work on this topic has shown that centromeric transcripts are found across the eukaryotic tree and associate with heterochromatin formation, chromatin structure, kinetochore structure, centromeric protein loading, and inner centromere signaling. In this review, we discuss the conservation of small and long non-coding centromeric RNAs, their associations with various centromeric functions, and their potential roles in disease.

Molecular dynamics simulations of DNA-DNA and DNA-protein interactions

The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA-protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest.

Liquid-like interactions in heterochromatin: Implications for mechanism and regulation

A large portion of the eukaryotic genome is packed into heterochromatin, a versatile platform that is essential to maintain genome stability. Often associated with a compact and transcriptionally repressed chromatin state, heterochromatin was earlier considered a static and locked compartment. However, cumulative findings over the last 17 years have suggested that heterochromatin displays dynamics at different timescales and size scales. These dynamics are thought to be essential for the regulation of heterochromatin. This review illustrates how the key principles underlying heterochromatin structure and function have evolved along the years and summarizes the discoveries that have led to the continuous revision of these principles. Using heterochromatin protein 1-mediated heterochromatin as a context, we discuss a novel paradigm for heterochromatin organization based on two emerging concepts, phase separation and nucleosome structural plasticity. We also examine the broader implications of this paradigm for chromatin organization and regulation beyond heterochromatin.

Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes

Histone variants regulate replication, transcription, DNA damage repair, and chromosome segregation. Though widely accepted as a paradigm, it has not been rigorously demonstrated that histone variants encode unique mechanical properties. Here, we present a new theoretical approach called minimal cylinder analysis that uses strain fluctuations to determine the Young's modulus of nucleosomes from all-atom molecular dynamics simulations. Recently, we validated this computational tool against in vitro single-molecule nanoindentation of histone variant nucleosomes. In this report, we further extend minimal cylinder analysis to study the biophysical properties of hybrid nucleosomes that are known to exist in human cancer cells and contain H3 histone variants CENP-A and H3.3. Here, we report that the heterotypic nucleosome has an intermediate elasticity (8.5 ± 0.5 MPa) compared to CENP-A (6.2 ± 0.4 MPa) and H3 (9.8 ± 0.7 MPa) and that the dynamics of both canonical and CENP-A nucleosomes are preserved and partitioned across the nucleosome pseudodyad. Furthermore, we investigate the mechanism by which the elasticity of these heterotypic nucleosomes augments cryptic binding surfaces. From these analyses, we predict that the heterotypic nucleosome is permissive to the binding of one copy of the kinetochore protein CENP-C while still retaining a closed DNA end configuration required for linker histone H1 to bind. We discuss that the ectopic deposition of CENP-A in cancer by H3.3 chaperones HIRA and DAXX may fortuitously result in hybrid nucleosome formation. Using these results, we propose biological outcomes that might arise when such heterotypic nucleosomes occupy large regions of the genome.

Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling

Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression. It consists of a complex network of DNA and proteins whose characteristic dynamical modes facilitate compaction and rearrangement in the cell nucleus. These modes stem from chromatin's fundamental unit, the nucleosome, and their effects are propagated across length scales. Understanding the effects of nucleosome dynamics on the chromatin fiber, primarily through post-translational modifications that occur on the histones, is of central importance to epigenetics. Within the last decade, imaging and chromosome conformation capture techniques have revealed a number of structural and statistical features of the packaged chromatin fiber at a hitherto unavailable level of resolution. Such experiments have led to increased efforts to develop polymer models that aim to reproduce, explain, and predict the contact probability scaling and density heterogeneity. At nanometer scales, available models have focused on the role of the nucleosome and epigenetic marks on local chromatin structure. At micrometer scales, existing models have sought to explain scaling laws and density heterogeneity. Less work, however, has been done to reconcile these two approaches: bottom-up and top-down models of chromatin. In this perspective, we highlight the multiscale simulation models that are driving toward an understanding of chromatin structure and function, from the nanometer to the micron scale, and we highlight areas of opportunity and some of the prospects for new frameworks that bridge these two scales. Taken together, experimental and modeling advances over the last few years have established a robust platform for the study of chromatin fiber structure and dynamics, which will be of considerable use to the chromatin community in developing an understanding of the interplay between epigenomic regulation and molecular structure.

Job Opening for Nucleosome Mechanic: Flexibility Required

The nucleus has been studied for well over 100 years, and chromatin has been the intense focus of experiments for decades. In this review, we focus on an understudied aspect of chromatin biology, namely the chromatin fiber polymer’s mechanical properties. In recent years, innovative work deploying interdisciplinary approaches including computational modeling, in vitro manipulations of purified and native chromatin have resulted in deep mechanistic insights into how the mechanics of chromatin might contribute to its function. The picture that emerges is one of a nucleus that is shaped as much by external forces pressing down upon it, as internal forces pushing outwards from the chromatin. These properties may have evolved to afford the cell a dynamic and reversible force-induced communication highway which allows rapid coordination between external cues and internal genomic function.

Polymer models for the mechanisms of chromatin 3D folding: review and perspective

In this perspective paper, classical physical models for mammalian interphase chromatin folding are reviewed.