Nuclear organisation and replication timing are coupled through RIF1–PP1 interaction

Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing programme and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. The role of RIF1 in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing programme and nuclear architecture.

Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation

Classification and characterisation of cellular morphological states are vital for understanding cell differentiation, development, proliferation and diverse pathological conditions. As the onset of morphological changes transpires following genetic alterations in the chromatin configuration inside the nucleus, the nuclear texture as one of the low-level properties if detected and quantified accurately has the potential to provide insights on nuclear organisation and enable early diagnosis and prognosis. This study presents a three dimensional (3D) nuclear texture description method for cell nucleus classification and variation measurement in chromatin patterns on the transition to another phenotypic state. The proposed approach includes third plane information using hyperplanes into the design of the Sorted Random Projections (SRP) texture feature and is evaluated on publicly available 3D image datasets of human fibroblast and human prostate cancer cell lines obtained from the Statistics Online Computational Resource. Results show that 3D SRP and 3D Local Binary Pattern provide better classification results than other feature descriptors. In addition, the proposed metrics based on 3D SRP validate the change in intensity and aggregation of heterochromatin on transition to another state and characterise the intermediate and ultimate phenotypic states.

Form from Function, Order from Chaos in Male Germline Chromatin

Spermatogenesis requires radical restructuring of germline chromatin at multiple stages, involving co-ordinated waves of DNA methylation and demethylation, histone modification, replacement and removal occurring before, during and after meiosis. This Special Issue has drawn together papers addressing many aspects of chromatin organization and dynamics in the male germ line, in humans and in model organisms. Two major themes emerge from these studies: the first is the functional significance of nuclear organisation in the developing germline; the second is the interplay between sperm chromatin structure and susceptibility to DNA damage and mutation. The consequences of these aspects for fertility, both in humans and other animals, is a major health and social welfare issue and this is reflected in these nine exciting manuscripts.

Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction

Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing program and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. RIF1’s role in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing program and nuclear architecture.

The role of chromosome segregation and nuclear organisation in human subfertility

Spermatogenesis is central to successful sexual reproduction, producing large numbers of haploid motile male gametes. Throughout this process, a series of equational and reductional chromosome segregation precedes radical repackaging of the haploid genome. Faithful chromosome segregation is thus crucial, as is an ordered spatio-temporal ‘dance’ of packing a large amount of chromatin into a very small space. Ergo, when the process goes wrong, this is associated with an improper chromosome number, nuclear position and/or chromatin damage in the sperm head. Generally, screening for overall DNA damage is relatively commonplace in clinics, but aneuploidy assessment is less so and nuclear organisation studies form the basis of academic research. Several studies have focussed on the role of chromosome segregation, nuclear organisation and analysis of sperm morphometry in human subfertility observing significant alterations in some cases, especially of the sex chromosomes. Importantly, sperm DNA damage has been associated with infertility and both extrinsic (e.g. lifestyle) and intrinsic (e.g. reactive oxygen species levels) factors, and while some DNA-strand breaks are repaired, unexpected breaks can cause differential chromatin packaging and further breakage. A ‘healthy’ sperm nucleus (with the right number of chromosomes, nuclear organisation and minimal DNA damage) is thus an essential part of reproduction. The purpose of this review is to summarise state of the art in the fields of sperm aneuploidy assessment, nuclear organisation and DNA damage studies.

Ultrastructure of ovarian germ cells in the ostrich (Struthio camelus) embryo

In this study, the ultrastructural development of germ cells in the ostrich embryo was analysed. The nuclear organisation and morphological characteristics of cytoplasm in the developing germ cells, on embryonic days 20, 26, and 36 and the day of hatching (5 samples from each stage) was analysed using transmission electron microscopy (TEM). Germ cells located in the cortex of left ovaries were identified by their large size and centrally located nucleus, with a conspicuous nucleolus. In these cells, the cytoplasm contained an abundance of mitochondria and free ribosomes. The structure of Balbiani body, a villous-like elevation in wide intercellular space and desmosome junction between two adjacent germ cells was also studied. The germ cells during embryonic development showed structural differences in both the nucleus and cytoplasm.

Lamina and Heterochromatin Direct Chromosome Organisation in Senescence and Progeria

Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we use simulations based on concepts from polymer physics to dissect the roles played by heterochromatin- and lamina-mediated interactions in nuclear organisation. Our model explains the conventional organisation of heterochromatin and euchromatin in growing cells, as well as the pathological organisation found in oncogene-induced senescence and progeria. We show that the experimentally observed changes in the locality of contacts in senescent and progeroid cells can be explained naturally as arising due to phase transitions in the system. Our model predicts that LADs are highly stochastic, and that, once established, the senescent phenotype should be metastable even if lamina-mediated interactions were reinstated. Overall, our simulations uncover a universal physical mechanism that can regulate heterochromatin segregation and LAD formation in a wide range of mammalian nuclei.