Changes In Chromosome Organization Research Articles

Replicating Chromosomes in Whole-Cell Models of Bacteria.

Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication of genetic material. In a recent study, we presented a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics. This approach was used to investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell cycle. To achieve cell-scale chromosome structures that are realistic, we modeled the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. Additionally, the polymer interacts with ribosomes distributed according to cryo-electron tomograms of Syn3A. The polymer model was further augmented by computational models of loop extrusion by structural maintenance of chromosomes (SMC) protein complexes and topoisomerase action, and the modeling and analysis of multi-fork replication states.

Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation

BackgroundGenomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized.ResultsAccordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the ‘fatty acid metabolism’, ‘response to stress’, ‘carbon fixation’ and ‘photosynthesis’ functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression.ConclusionsOverall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.

Dynamics of chromosome organization in a minimal bacterial cell.

Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.

Structural changes in chromosomes driven by multiple condensin motors during mitosis

We create a computational framework that utilizes loop extrusion (LE) by multiple condensin I/II motors to predict changes in chromosome organization during mitosis. The theory accurately reproduces the experimental contact probability profiles for the mitotic chromosomes in HeLa and DT40 cells. The LE rate is smaller at the start of mitosis and increases as the cells approach metaphase. Condensin II-mediated mean loop size is about six times larger than loops because of condensin I. The loops, which overlap each other, are stapled to a central dynamically changing helical scaffold formed by the motors during the LE process. A polymer physics-based data-driven method that uses the Hi-C contact map as the only input shows that the helix is characterized as random helix perversions (RHPs) in which the handedness changes randomly along the scaffold. The theoretical predictions, which are testable using imaging experiments, do not contain any parameters.

Molecular Link between DNA Damage Response and Microtubule Dynamics.

Microtubules are major components of the cytoskeleton that play important roles in cellular processes such as intracellular transport and cell division. In recent years, it has become evident that microtubule networks play a role in genome maintenance during interphase. In this review, we highlight recent advances in understanding the role of microtubule dynamics in DNA damage response and repair. We first describe how DNA damage checkpoints regulate microtubule organization and stability. We then highlight how microtubule networks are involved in the nuclear remodeling following DNA damage, which leads to changes in chromosome organization. Lastly, we discuss how microtubule dynamics participate in the mobility of damaged DNA and promote consequent DNA repair. Together, the literature indicates the importance of microtubule dynamics in genome organization and stability during interphase.

Characterization of some satellite DNA families in Deschampsia antarctica (Poaceae)

Deschampsia antactica E. Desv. is one of the only two native vascular plants of Antarctica, having a disjunct distribution with South America. Its presence in different environmental conditions turns it into an interesting evolution model, particularly for genomic evolutionary studies. The repetitive DNA is a genome component that cause important changes in genome size and chromosome organization, and therefore, its variation is very important in group’s delimitation. Some tandem repetitive DNA sequences, known as satellite DNA (satDNAs) are shared between many groups of Poaceae (e.g., of these are the CON1, CON2, COM1, and COM2 sequences) highlighting its evolutionary component. This study aims to identify, classify, and characterize repetitive elements in the D. antarctica genome by clustering analysis of genome sequences, focusing on the CON1, CON2, COM1, and COM2. Repetitive DNA represented about 73.3% of the D. antarctica genome. All studied populations presented loci for the studied satDNAs but the distribution pattern showed differences that seem to be related to the geographic distribution. The analysis of CON/COM sequences in D. antarctica contributes to the understanding of these elements in Poaceae genomes and highlights the importance of changes in chromosome organization of repetitive DNA in populations with fragmented geographical distribution. The distribution of such chromosome changes may both reflect the process of colonization of D. antarctica in Antarctica and explain some evolutionary processes of differentiation in Deschampsia species complex in the Patagonia, which is still unresolved with other DNA sequences.

Novel insights into mitotic chromosome condensation.

The fidelity of mitosis is essential for life, and successful completion of this process relies on drastic changes in chromosome organization at the onset of nuclear division. The mechanisms that govern chromosome compaction at every cell division cycle are still far from full comprehension, yet recent studies provide novel insights into this problem, challenging classical views on mitotic chromosome assembly. Here, we briefly introduce various models for chromosome assembly and known factors involved in the condensation process (e.g. condensin complexes and topoisomerase II). We will then focus on a few selected studies that have recently brought novel insights into the mysterious way chromosomes are condensed during nuclear division.

Hubert Rees DFC. 2 October 1923 — 13 September 2009

Hubert Rees was born on 2 October 1923 in Llangennech, Carmarthenshire, in Wales, and died on 13 September 2009 in Aberystwyth. Hugh, as he was known to his wide circle of friends and colleagues, was educated at Llandovery and Llanelli grammar schools. After leaving school he joined the Royal Air Force (RAF) and in 1944 he became a Lancaster bomber pilot. On demobilization in 1946 he enrolled as a student at Aberystwyth University, graduating with first-class honours in agricultural botany in 1950. After a short secondment to the John Innes Horticultural Institution at Bayfordbury he took up an appointment as Lecturer in Cytology at the newly-formed Department of Genetics at Birmingham University. In 1958 he returned to Aberystwyth as Senior Lecturer in Agricultural Botany, being promoted to Reader in 1966 and ultimately Professor and Head of Department. He rapidly built up an internationally acclaimed school of study into the genetic control of chromosome behaviour in plants, and on evolutionary changes in chromosome organization. Hugh Rees had an impressive intellect and was an inspirational teacher who left his mark on all who came under his supervision. In 1983 he was appointed Vice Principal at Aberystwyth. He retired in 1991 and then pursued his many interests and hobbies. Together with his wife, Mavis, he was well known to many friends and colleagues for his generous hospitality, his love of good food and wine, and as a raconteur. Hugh is survived by his wife, a son and two daughters. Another son predeceased him.

Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH

During interphase, chromosomes are arranged into territories within a highly organized nuclear space containing several compartments. It is becoming clear that this complex nuclear arrangement is important for gene regulation and therefore expression. The study of chromosome organization in interphase requires high-resolution imaging methods that at the same time allow for flexible labelling strategies and preserve nuclear structure. Tokuyasu cryosections of cells or tissues provide a simple, high-resolution platform for performing immunolabelling and fluorescence in situ hybridization (FISH) on well-preserved samples. Here we show how FISH performed on thin cryosections (cryo-FISH) can be used for the study of chromosome organization at high resolution and in a quantitative manner. We have measured chromosome intermingling, volume and radial position, in resting and activated human lymphocytes, and observed chromosome-specific differences between the two cellular states. These differences are in part related to the nuclear expansion that occurs during activation, but are also likely to be tied to their different transcriptional profiles. Extrapolation of our dataset to the whole genome suggests that activated cells contain a lower amount of chromatin involved in intermingling than resting cells.

Chromatin organization and virus gene expression

Many viruses introduce DNA into the host-cell nucleus, where they must either embrace or confront chromatin factors as a support or obstacle to completion of their life cycle. Compared to the eukaryotic cell, viruses have compact and rapidly evolving genomes. Despite their smaller size, viruses have complex life cycles that involve dynamic changes in DNA structure. Nuclear entry, transcription, replication, genome stabilization, and virion packaging involve complex changes in chromosome organization and structure. Chromatin dynamics and epigenetic modifications play major roles in viral and host chromosome biology. In some cases, viruses may use novel or viral-specific epigenetic modifying activities, which may reflect variant pathways that distinguish their behavior from the bulk of the cellular chromosome. This review examines several recent discoveries that highlight the role of chromatin dynamics in the life cycle of DNA viruses.

Alternative ends: Telomeres and meiosis

Meiosis is a specialized type of cell division that halves the diploid number of chromosomes, yielding four haploid nuclei. Dramatic changes in chromosomal organization occur within the nucleus at the beginning of meiosis which are followed by the separation of homologous chromosomes at the first meiotic division. This is the case for telomeres that display a meiotic-specific behavior with gathering in a limited sector of the nuclear periphery. This leads to a characteristic polarized chromosomal configuration, called the “bouquet” arrangement. The widespread phenomenon of bouquet formation among eukaryotes has led to the hypothesis that it is functionally linked to the process of interactions between homologous chromosomes that are a unique feature of meiosis and are essential for proper chromosome segregation. Various studies in different model organisms have questioned the role of the telomere bouquet in chromosome pairing and recombination, and very recently in meiotic spindle formation, and have provided some clues about the molecular mechanisms that carry out this specific clustering of telomeres.

Crossover interference

Crossover interference

The Role of Constitutive and Inducible Processes in the Response of Human Squamous Cell Carcinoma Cell Lines to Ionizing Radiation

The inherent radiation sensitivity of the cells within a tumor is thought to contribute to the success or failure of radiation therapy. In vitro studies have shown that differences in the radiation sensitivity of squamous cell carcinoma cell lines reflect alterations in DNA repair. These alterations result from constitutive changes in chromosome organization, not radiation-inducible processes. While inducible responses may play some role in the radiation response of tumor cells, there is no evidence for their involvement in inherent differences in tumor cell radiosensitivity or in the success or failure of radiotherapy of squamous cell carcinomas.

The Rockefeller Foundation and spectroscopy research: the programs at Chicago and Utrecht.

The introduction of new experimental or analytical tools into programs of scientific research can be the spur for advancing and deepening scientific understanding. In the life sciences, for example, the use of the microscope to examine cells from organisms that previously had been studied only by genetic crossing allowed changes in chromosomal organization to be correlated with the inheritance of specific physical features, thereby stimulating the elaboration of new theories of evolutionary change. Similarly, the use of chemical and physical manipulations on embryos whose developmental changes had been meticulously followed only with microscopic techniques permitted new types of insights into embryological changes and opened up new categories of questions about the regulation of differentiation and development. Decisions to employ new techniques and strike out in novel and uncertain directions have generally been individual ones made by single investigators in response to their own perceived research needs. In the mid-1930s the Natural Sciences division of the Rockefeller Foundation, under the direction of Warren Weaver, began a major initiative to improve research in the biological sciences by bringing the tools of the physical sciences into biological investigations.' At that time, the Rockefeller Foundation had made sup-

Meiotic chromosome structure. Kinetochores and chromatid cores in standard and B chromosomes of Arcyptera fusca (Orthoptera) revealed by silver staining

The behaviour of two chromosome structures in silver-stained chromosomes was analyzed through the first meiotic division in spermatocytes of the acridoid species Arcyptera fusca. Results showed that at diakinesis kinetochores and chromatid cores are individualized while they associate in bivalents of metaphase I; only kinetochores and distal core spots associate in the sex chromosome. Metaphase I is characterized by morphological and localization changes of both kinetochores and cores which define the onset of anaphase I. These changes analyzed in both autosomes and in the sex chromosome allow us to distinguish among three different substages in metaphase I spermatocytes. B chromosomes may be present as univalents, bivalents, or trivalents. Metaphase I B univalents are characterized by separated cores except at their distal ends and individualized and flat sister kinetochores. At anaphase I sister kinetochores of lagging B chromatids remain connected through a silver-stained strand. The behaviour of cores and kinetochores of B bivalents is identical with that found in the autosomal bivalents. The differences in the morphology of kinetochores of every chromosome shown by B trivalents at metaphase I may be related to the balanced forces acting on the multivalent. The results show dramatic changes in chromosome organization of bivalents during metaphase I. These changes suggest that chromatid cores are not involved in the maintenance of bivalents. Moreover, the changes in morphology of kinetochores are independent of the stage of meiosis but correlate with the kind of division (amphitelic-syntelic) that chromosomes undergo.

A nuclear body in meiosis of Bromus

1. A structure which is tentatively called a “nuclear body” has been observed in microsporocytes in a large number of species of Bromus. It was found in diploid and polyploid species and in species with complements of large (L-)chromosomes, medium (M-)chromosomes or L- and M-chromosomes. These species were collected in North and South America and Europe. It is suggested that the nuclear body occurs regularly in species of the genus Bromus. 2. The nuclear body was first visible at pachytene. It was generally single. In some individuals it disappeared at the end of prophase; in others it was present during later stages of meiosis, in some instances as late as the quartet. The nuclear body was not observed when the quartet cells had separated. Before it disappeared the nuclear body underwent a sudden or gradual diminution. It decreased in size, or became faint-staining and faded away; or it decreased in size and faded. The nuclear body generally disappeared at the end of prophase in the diploid and tetraploid species and was present at metaphase-I and later stages in higher polyploid species. 3. When the nuclear body was present in later stages of meiosis it behaved as follows: It was extruded from the spindle at metaphase-I and frequently came to lie in the polar region of the cell; it was not included in either nucleus at telophase-I. A single nuclear body was present in one dyad cell; it lay outside the spindle at metaphase-II, and was included in one of the cells of the quartet. 4. A very great range in the size of the nuclear body was found in early stages of meiosis. Some variation in size was found within individuals and among individuals of the same species. Present data indicate some relationship between chromosome number and size of the nuclear body. The largest nuclear bodies were found in duodecaploid and octoploid and the smallest in diploid species; however an exact correspondence was not observed. 5. The nuclear body is extremely variable in shape. It has a vesicular appearance; there is great variation in the number, size and staining of the vesicles. The appearance of the nuclear body may vary within and among anthers and individuals. 6. The nuclear body is not associated with the nucleolus at pachytene, nor with the nucleolar organizing regions of specific bivalents. The nuclear body is often touching a bivalent or attached by fine strands to a bivalent during prophase. However, there appears to be no specifically differentiated region of any bivalent with which it is generally associated. The nuclear body may be associated with terminal or interstitial regions of bivalents which differ in size or chromomere pattern. It was more frequently associated with bivalents in some individuals than others. 7. The nuclear body was not found in mitotic divisions in shoot or root tips and thus appears to be related specifically to the meiotic divisions. It may arise as an exudate from some chromosomes, or it may be extruded from the nucleolar material; it seems less likely to arise from the karyolymph. It may be composed of some materials discarded in preparation for meiosis or during its earliest stages, which are perhaps related to concurrent changes in chromosome organization. 8. Observations are considered which suggest that a structure similar to the nuclear body observed in Bromus may be present in other plant genera.