Organization and Dynamics of Chromosomes.

BackgroundThe development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics and computational biology. Aided by high-throughput next generation sequencing techniques, the Hi-C technique can generate genome-wide, large-scale intra- and inter-chromosomal interaction data capable of describing in details the spatial interactions within a genome. These data can be used to reconstruct 3D structures of chromosomes that can be used to study DNA replication, gene regulation, genome interaction, genome folding, and genome function.ResultsHere, we introduce a maximum likelihood algorithm called 3DMax to construct the 3D structure of a chromosome from Hi-C data. 3DMax employs a maximum likelihood approach to infer the 3D structures of a chromosome, while automatically re-estimating the conversion factor (α) for converting Interaction Frequency (IF) to distance. Our results show that the models generated by 3DMax from a simulated Hi-C dataset match the true models better than most of the existing methods. 3DMax is more robust to structural variability and noise. Compared on a real Hi-C dataset, 3DMax constructs chromosomal models that fit the data better than most methods, and it is faster than all other methods. The models reconstructed by 3DMax were consistent with fluorescent in situ hybridization (FISH) experiments and existing knowledge about the organization of human chromosomes, such as chromosome compartmentalization.Conclusions3DMax is an effective approach to reconstructing 3D chromosomal models. The results, and the models generated for the simulated and real Hi-C datasets are available here: http://sysbio.rnet.missouri.edu/bdm_download/3DMax/. The source code is available here: https://github.com/BDM-Lab/3DMax. A short video demonstrating how to use 3DMax can be found here: https://youtu.be/ehQUFWoHwfo.

Remarkable progress has been made in understanding chromosome structures inside the cell nucleus. Recent advances in Hi-C technologies enable the detection of genome-wide chromatin interactions, providing insight into three-dimensional (3D) genome organization. Advancements in the spatial and temporal resolutions of imaging as well as in molecular biological techniques allow the tracking of specific chromosomal loci, improving our understanding of chromosome movements. From these data, we are beginning to understand how the intra-nuclear locations of chromatin loci and the 3D genome structure change during development and differentiation. This emerging field of genome structure and dynamics research requires an interdisciplinary approach including efficient collaborations between experimental biologists and physicists, informaticians, or engineers. Quantitative and mathematical analyses based on polymer physics are becoming increasingly important for processing and interpreting experimental data on 3D chromosome structures and dynamics. In this review, we aim to provide an overview of recent research on the physical aspects of chromosome structure and dynamics oriented for biologists. These studies have mainly focused on chromosomes at the cellular level, using unicellular organisms and cultured cells. However, physical parameters that change during development, such as nuclear size, may impact genome structure and dynamics. Here, we discuss how chromatin dynamics and genome structures in early embryos change during development, which we expect will be a hot topic in the field of chromatin dynamics in the near future. We hope this review helps developmental biologists to quantitatively investigate the physical natures of chromosomes in developmental biology research.

During mitosis in eukaryotes, the nuclear genome is organized into highly condensed structures referred to as chromosomes. The dynamic processes of chromosome condensation and segregation play crucial roles in the equal separation of genetic information to both daughter cells. Since disruption of these processes is harmful to cells, causing, for example, chromosome aneuploidy, appropriate regulation is indispensable. Chromosome dynamics involves modification of the molecules that regulate these processes during mitosis. The usefulness of tobacco BY-2 (Nicotiana tabacum cv. Bright Yellow-2) cultured cells in analyses of chromosome dynamics has been recently demonstrated. Tobacco BY-2 cells possess the following advantages. Their mitotic chromosomes are not small and monocentric, which is advantageous because analyses of chromosome dynamics are generally performed under a microscope. Thehaploid genome size of the amphidiploid speciesNicotiana tabacum (2n = 4x = 48) is about 4,500Mb (Arumuganathan and Earle 1991) and the total nuclear genome is divided into 48 mitotic chromosomes. The length of thesemitotic chromosomes varies from 2 to 6 μm (Kenton et al. 1993;Moscone et al. 1996), which is larger than that in Arabidopsis thaliana (c.a. 2 μm). Such chromosome size makes it possible to analyze the detailed morphology and structure of chromosomes. Although BY-2 cultured cells are derived from N. tabacum, it is probable that a certain level of ploidy change and chromosome abnormality occurs during cell culture. However, any problem encountered in studies of chromosome dynamics has not been reported to date. Another advantage of tobaccoBY-2 cells is their ability for high synchronization. Because mitotic chromosomes only emerge in the short mitotic phase, synchronous cell systems are very useful for studying chromosome dynamics. A highly synchronous method has been established in tobacco BY-2 cells (Nagata et al. 1992) and the usefulness of synchronized BY-2 cells has been widely demonstrated inplant cell cycle studies (Ito 2000). SynchronizedBY-2 cells provide the most efficient mitotic chromosomes because a mitotic index of more

Editor's evaluation: Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus

Decision letter: Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus

Mitosis and cytokinesis are fundamental processes through which somatic cells increase their numbers and allow plant growth and development. Here, we analyzed the organization and dynamics of mitotic chromosomes, nucleoli, and microtubules in living cells of barley root primary meristems using a series of newly developed stable fluorescent protein translational fusion lines and time-lapse confocal microscopy. The median duration of mitosis from prophase until the end of telophase was 65.2 and 78.2 min until the end of cytokinesis. We showed that barley chromosomes frequently start condensation before mitotic pre-prophase as defined by the organization of microtubules and maintain it even after entering into the new interphase. Furthermore, we found that the process of chromosome condensation does not finish at metaphase, but gradually continues until the end of mitosis. In summary, our study features resources for in vivo analysis of barley nuclei and chromosomes and their dynamics during mitotic cell cycle.

Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with ~180,000 copies per cell. Dps binds DNA and oxidises iron, facilitating survival in harsh environments. Dps-DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganises the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that after 96 h of starvation, Dps compacts the nucleoid and increases short-range DNA-DNA interactions, but does not affect chromosome accessibility to large protein nanocages or small restriction enzymes. We also report that chromosome dynamics and organisation are primarily impacted by the bacterial growth phase; the effect of Dps is relatively minor. Our work clarifies the role of Dps in modulating nucleoid properties, and we propose an updated model for Dps-DNA interactions in which Dps binds, protects and compacts DNA largely without influencing chromosome access, dynamics and organisation. Additionally, this work provides a general framework for assessing the impact of nucleoid-associated proteins on key aspects of chromosome function in live cells.

This chapter explains the chromosome organization and dynamics in bacteria. It reviews some of the main discoveries and open questions on the bacterial chromosome that emerged from studies, through the experimental, theoretical and computational work performed around them. The chapter highlights research directions in this area where theoretical and experimental work performed on bacteria can lead the way to formulating new questions concerning eukaryotic chromosomes, and, vice versa, attempt to identify where studies performed on eukaryotes can inform the field of the bacterial chromosome. It explores the four different but inter-related areas of chromosome folding, deoxyribonucleic acid-organizing proteins, chromosome dynamics, and role of molecular crowding, presented in separate sections. Molecular dynamics simulations with simple but explicit descriptions of crowders are available, and allow, for example, the study of the role of size and polydispersity of crowding agents on chromosome compaction.

Conformational ensembles of biopolymers, whether proteins or chromosomes, can be described using contact matrices. Principal component analysis (PCA) on the contact data has been used to interrogate both protein and chromosome structures and/or dynamics. However, as these fields have developed separately, variants of PCA have emerged. Previously, a variant we hereby term Implicit-PCA (I-PCA) has been applied to chromosome contact matrices and revealed the spatial segregation of active and inactive chromatin. Separately, Explicit-PCA (E-PCA) has previously been applied to proteins and characterized their correlated structure fluctuations. Here, we swapped analysis methods (I-PCA and E-PCA), applying each to a different biopolymer type (chromosome or protein) than the one for which they were initially developed. We find that applying E-PCA to chromosome distance matrices derived from microscopy data can reveal the dominant motion (concerted fluctuation) of these chromosomes. Further, by applying E-PCA to Hi-C data across the human blood cell lineage, we isolated the aspects of chromosome structure that most strongly differentiate cell types. Conversely, when we applied I-PCA to simulation snapshots of proteins, the major component reported the consensus features of the structure, making this a promising approach for future analysis of semi-structured proteins.

Author SummaryMitotic chromosomes of eukaryotes are relatively large rod-like cellular organelles, about 1 µm in diameter and 10 µm long, of well-studied composition but unknown structure. The question of whether all DNA sequences equally contribute to the interactions leading to the formation of mitotic chromosomes has never been asked. To find an answer, we determined whether the radial positions of specific chromatin loci within mitotic chromosomes were reproduced at every cell cycle or were purely random. Based on fluorescence microscopy images of live or fixed chromosomes in cells from Drosophila embryos or Drosophila larval tissues expressing the MSL3-GFP fusion protein from a transgene, we report that the large-scale organization of mitotic chromosomes is reproduced not only longitudinally, as in the well-known chromosome banding phenomenon, but also radially. Actively transcribed, dosage-compensated genes of the Drosophila male X chromosome were always found at the periphery of mitotic chromosomes, starting from late prophase. Histone modifications specific to active chromatin were found to be more peripheral compared to silent chromatin that tended to be more central in the condensed chromosome. These findings are both exciting and significant for the field of cell and chromatin biology because they may help reconcile the old controversy between the existing models of chromosome structure that posit either radial loops of chromatin or consecutive coiling. In addition, we offer new insights into the mechanisms of mitotic condensation and suggest a link between structural and functional roles of different chromatin domains.

Recent Advances in Plant Cell Nuclear Signaling

Chromosome organization and dynamics in plants

The three-dimensional (3D) structure of chromosomes is of great significance to ensure that the genome performs various functions (e.g., gene expression) correctly and replicates and separates correctly in mitosis. Since the emergence of Hi-C in 2009, a new experimental technique in molecular biology, researchers have been paying more and more attention to the reconstruction of chromosome 3D structure. To reconstruct the 3D structure of chromosomes based on Hi-C experimental data, many algorithms have been proposed, among which ShRec3D is one of the most outstanding. In this article, an iterative ShRec3D algorithm is presented to greatly improve the native ShRec3D algorithm. Experimental results show that our algorithm can significantly promote the performance of ShRec3D, and this improvement is applicable to almost all data noise range and signal coverage range, so it is universal.

In developing coarse-grained (CG) polymer models it is important to reproduce both local and molecule-scale structure. We develop a procedure for fast calculation of the bond-orientation correlation and the internal squared distance 〈R^{2}(M)〉 through evaluation of the probability distribution functions that represent a CG model. Different CG models inherently contain or omit correlations between CG variables. Here, we construct CG models that contain specific correlations between CG variables. The importance of different correlations is tested on CG models of polyethylene, polytetrafluoroethylene, and poly-L-lactic acid. The chain stiffness and 〈R^{2}(M)〉 are calculated using both analytic evaluation and Monte Carlo sampling, and approximate model results are compared with exact results from all-atom simulations. For polymers with an exponential correlation decay, the bond-orientation correlation and 〈R^{2}(M)〉 indicate which CG variable correlations are most important to reproduce molecule-scale structure. Analysis of the bond-orientation correlation and internal-squared distance indicates that for poly-L-lactic acid the bond-orientation correlation requires qualitatively different additional terms in CG models and quantifies the error in neglecting this important behavior.

We develop a systematic coarse-grained (CG) model for methylcellulose polymers, including random copolymers with compositions representative of modeling commercial METHOCEL A polymer, using one CG bead per monomer. We parametrize our CG model using the RDFs from atomistic simulations of short methylcellulose oligomers, extrapolating the results to long chains. Using a LJ 9–6 potential, the CG model captures the effect of monomer substitution type and temperature observed in detailed atomistic simulations. We use dissociation free energy to validate our CG model against the atomistic model. We then use this CG model to simulate single chains up to 1000 monomers long, and we calculate persistence lengths for a selection of homogeneous and heterogeneous methylcellulose chains, which show good agreement with experimental results. Interestingly, simulations of 600-mer heterogeneous chains show a collapse transition at 50 °C and form a stable ring structure with outer diameter around 14 nm. This structure appea...