Identical Genetic Information Research Articles

Vacuolar H+-ATPase determines daughter cell fates through asymmetric segregation of the nucleosome remodeling and deacetylase complex.

Asymmetric cell divisions (ACDs) generate two daughter cells with identical genetic information but distinct cell fates through epigenetic mechanisms. However, the process of partitioning different epigenetic information into daughter cells remains unclear. Here, we demonstrate that the nucleosome remodeling and deacetylase (NuRD) complex is asymmetrically segregated into the surviving daughter cell rather than the apoptotic one during ACDs in Caenorhabditis elegans. The absence of NuRD triggers apoptosis via the EGL-1-CED-9-CED-4-CED-3 pathway, while an ectopic gain of NuRD enables apoptotic daughter cells to survive. We identify the vacuolar H+-adenosine triphosphatase (V-ATPase) complex as a crucial regulator of NuRD's asymmetric segregation. V-ATPase interacts with NuRD and is asymmetrically segregated into the surviving daughter cell. Inhibition of V-ATPase disrupts cytosolic pH asymmetry and NuRD asymmetry. We suggest that asymmetric segregation of V-ATPase may cause distinct acidification levels in the two daughter cells, enabling asymmetric epigenetic inheritance that specifies their respective life-versus-death fates.

Different Phenotypes in Monozygotic Twins, Carriers of the Same Pathogenic Variant for Hypertrophic Cardiomyopathy.

Hypertrophic cardiomyopathy (HCM) is a monogenic disease with autosomal dominant inheritance. Genotype–phenotype relationships are complex, with variable penetrance even within the same family. The involvement of other modulating genetic and environmental factors is unknown. We aimed to analyze the HCM in monozygotic twins, carriers of the same founder pathogenic variant MYBPC3 p.G263*. The relationship was verified using the PowerPlex 16 HS System kit. Phenotypic differences and environmental differences (overloading conditions, coexistence and location, lifestyle, sport, and intensity) were analyzed. Three pairs of twins genetically identical for all markers and carriers of MYBPC3 G263* were identified. No environmental differences were identified. One of the 89-year-old twins had symptomatic severe obstructive HCM that required septal ablation, while her twin has remained asymptomatic with mild phenotype >80 years. A 49-year-old twin had a severe phenotype of obstructive HCM and pending myectomy, while his twin had a mild asymptomatic phenotype. In the last pair of twins, one presented a much larger left ventricular hypertrophy than his identical twin. In summary, we present three pairs of HCM twin patients sharing not only the genetic cause of the inherited disease but the entire genetic background. Despite identical genetic information and the absence of other known clinical, environmental, or lifestyle differences, the severity of the HCM phenotype is strikingly different. These unexplained differences should prompt the study of other unknown modulating factors, either epigenetic or environmental.

Breaking Symmetry: The Asymmetries in Epigenetic Inheritance.

Symmetry and asymmetry are fundamental aspects of life. Most cells within a multicellular organism contain the same genetic information, passed on from one originating cell - the zygote; however, these cells can take on a variety of different identities, with diverse appearances and functions. A fundamental question in biology ponders how cells containing identical DNA content can take on different cell identities. Epigenetic mechanisms could be the symmetry breaking factor, as they are able to change gene expression in cells without changing the DNA sequence. While the process of duplication and segregation of DNA during cell division has been well studied, it is less understood how the epigenetic information is established and inherited in the cells within a multicellular organism. Studies of asymmetric stem cell division, where a stem cell division gives rise to a self-renewed stem cell and a differentiating daughter cell, provides a model to study how epigenetic information is maintained or changed to produce daughter cells with identical genetic information but distinct cell fates. Here, we discuss findings and ideas of how epigenetic information is maintained or changed during asymmetric cell division and the importance of this asymmetry in influencing cell fate.

MATHEMATICAL AND COMPUTER MODELLING REGULATORIKA OF HIERARCHICAL MOLECULAR-GENETIC SYSTEMS

The progress achieved in biology during the last century has led to development of mathematical and computer modelling of functioning regulatory mechanisms (regulatorika) in molecular-genetic processes in living systems. In this work we consider one of the possible methods for mathematical and computer mod- elling of molecular-genetic systems regulatorika. The corresponding equations (in the class of delay functional-differential equations) are developed, using the approaches by B.Goodwin, Bl. Sendov, M. Eigen, B.A. Ratner, and taking into account of tempo- rary relations, presence of multifunctional feedback and cooperative nature of processes in cell's regulatory loops. Results on the regulatorika for uniform molecular-genetic systems, as well as the problem of the origin and development of hierarchical molecular- genetic systems are considered. Results of using the considered method for analyzing cell's molecular-genetic systems in the presence of the alien genes (on the example of hepatic cell infections by hepatitis B virus) are given. 1 Introduction The analysis of main protein-ferments participating in the specific func- tioning of cells in a multicellular organism shows, that each cell contains different complex of protein molecules, though all cells have the same set of chromosomes and, consequently, identical genetic information (1, 2, 3). It happens because in eukaryotic cells there is mech- anism of hierarchical organizations of molecular-genetic system, regulating genes activity: which groups of genes at the moment must be active and which genes should be in the inactive condition. Existence of biochemical properties and processes, inherent all cells of the organism (syntheses of energy proteins, amino acid, to maintain and build membrane, etc) shows that there are universal groups of genes functioning in all cells regardless of specialization. Remaining part of genes consists of groups of general genes (its operation depends on activity conditions in universal groups of genes), containing information on general functions characteristic for many, but not all cells and groups of specific genes (its functioning depends on activity conditions of universal and general genes groups), keeping information on strictly specific functions of concrete cells (4). Under such approach, the whole cell genome of multicellular organism works as evolutionary established hierarchical system of universal, general and specific genes groups (Figure 1). Hierarchical organization of molecular-genetic systems is of the utmost importance in regulatorika of intracellular processes and cellular functions. Their account makes it possible to carry out studying mechanisms of origin, existence and development of living systems when quantitatively analyzing activity patterns of molecular-genetic systems. In this work we develop the mathematical modelling of genes activity (section 2), possible equations of molecular-genetic systems regulatorika (sections 3,4) and certain problems concerning the mathematical and computer modelling of hierarchical molecular-genetic systems (sections

Aberrant hydroxymethylation of ANGPTL4 is associated with selective intrauterine growth restriction in monochorionic twin pregnancies

ABSTRACT Selective intrauterine growth restriction (sIUGR) is a severe complication in monochorionic (MC) twin pregnancies, and it carries increased risks of poor prognosis. Current data suggest that vascular anastomoses and unequal placental sharing may be the key contributor to discordant foetal growth. While MC twins derive from a single zygote and have almost identical genetic information, the precise mechanisms remain unknown. DNA hydroxymethylation is a newly discovered epigenetic feature associated with gene regulation and modification. Here, we investigate discordant hydroxymethylation patterns between two placental shares of sIUGR and analyse the potential role of aberrant hydroxymethylation of angiopoietin-like 4 (ANGPTL4) in placental dysplasia. Hydroxymethylation DNA immunoprecipitation (hMeDIP)-chip and mRNA sequencing were performed to identify hydroxymethylation-associated genes. Real-time qPCR, western blotting, and immunohistochemistry were used to confirm ANGPTL4 expression. The mechanisms regulating ANGPTL4 were investigated by cell migration assay, invasion assay, viability assay, and apoptotic ratio assays, western blotting and hMeDIP-qPCR. Decreased ANGPTL4 was detected in the smaller placental shares of sIUGR. ANGPTL4 knockdown suppressed trophoblast invasiveness and migration, which possibly occurred through hypoxia inducible factor 1α (HIF-1α) and HIF-1 signalling pathway. Hypoxia leads to aberrant expression of ANGPTL4 and HIF-1α, positively correlated with their aberrant hydroxymethylation levels in promoter regions. Aberrant hydroxymethylation of ANGPTL4 may contribute to placental impairment by the HIF-1 signalling pathway in smaller placental shares of sIUGR.

Superresolution imaging of chromatin fibers to visualize epigenetic information on replicative DNA.

During DNA replication, the genetic information of a cell is copied. Subsequently, identical genetic information is segregated reliably to the two daughter cells through cell division. Meanwhile, DNA replication is intrinsically linked to the process of chromatin duplication, which is required for regulating gene expression and establishing cell identities. Understanding how chromatin is established, maintained or changed during DNA replication represents a fundamental question in biology. Recently, we developed a method to directly visualize chromatin components at individual replication forks undergoing DNA replication. This method builds upon the existing chromatin fiber technique and combines it with cell type-specific chromatin labeling and superresolution microscopy. In this method, a short pulse of nucleoside analog labels replicative regions in the cells of interest. Chromatin fibers are subsequently isolated and attached to a glass slide, after which a laminar flow of lysis buffer extends the lysed chromatin fibers parallel with the direction of the flow. Fibers are then immunostained for different chromatin-associated proteins and mounted for visualization using superresolution microscopy. Replication foci, or 'bubbles,' are identified by the presence of the incorporated nucleoside analog. For researchers experienced in molecular biology and superresolution microscopy, this protocol typically takes 2-3 d from sample preparation to data acquisition, with an additional day for data processing and quantification.

Use of ivacaftor in late diagnosed cystic fibrosis monozygotic twins heterozygous for F508del and R117H-7T \u2013 a case report

BackgroundCFTR modulator therapy with ivacaftor is a treatment option for Cystic Fibrosis (CF) patients with at least one copy of a R117H-7T mutation in the CFTR gene. Desirable effects of this therapy are improvement of lung function, decrease in exacerbation rate, normalization or reduction of sweat chloride and weight gain. Monogenetic CF-twins carry identical genetic information, so therapy response and side effects are expected to be nearly identical under this specific therapy.Case presentationIn monozygotic twins, at the age of 55, two pathogenic variants in the CFTR gene (F508del and R117H-7T) were detected. Both patients presented with a borderline sweat test (30–59 mmol/L) and despite the same genetic information and similar life circumstances the disease proceeds completely different. While one patient has severe pulmonary involvement with chronic P. aeruginosa infection, her twin sister is almost unimpaired. Liver or pancreatic involvement was not seen in either patient. Due to the presence of one copy of a R117H-7T mutation, CFTR modulator therapy with ivacaftor was initiated in both. Response and side effects were significantly different. In the less affected patient, we observed an improvement in lung function and a normalization of sweat chloride. In the severely affected patient, no functional response to treatment was seen, but stabilization of the disease state with a decrease in exacerbation and hospitalization rate and weight gain as well as a normalization of sweat chloride. There was an increase in liver enzymes in the less affected patient, which normalized after halving the dose of ivacaftor, while the therapeutic effect was maintained.ConclusionsDespite nearly identical genetic information, as in monogenetic twins, therapy response and onset of side effects of CFTR modulating therapy are very different. In patients with late diagnosis and severe pulmonary involvement, ivacaftor does not seem to improve lung function, whereas in patients with late diagnosis and low disease severity a relevant therapy response was obtained. In addition to lung function, additional clinical parameters such as reduction of exacerbation and hospitalization rate and weight gain should be used to assess therapy response, especially in severely affected patients.

The Unresolved Problem of DNA Bridging.

Accurate duplication and transmission of identical genetic information into offspring cells lies at the heart of a cell division cycle. During the last stage of cellular division, namely mitosis, the fully replicated DNA molecules are condensed into X-shaped chromosomes, followed by a chromosome separation process called sister chromatid disjunction. This process allows for the equal partition of genetic material into two newly born daughter cells. However, emerging evidence has shown that faithful chromosome segregation is challenged by the presence of persistent DNA intertwining structures generated during DNA replication and repair, which manifest as so-called ultra-fine DNA bridges (UFBs) during anaphase. Undoubtedly, failure to disentangle DNA linkages poses a severe threat to mitosis and genome integrity. This review will summarize the possible causes of DNA bridges, particularly sister DNA inter-linkage structures, in an attempt to explain how they may be processed and how they influence faithful chromosome segregation and the maintenance of genome stability.

Visualizing translational errors: one cell at a time.

Physiological heterogeneity among single cells with identical genetic information has been observed in a large number of bacterial phenotypes, including growth, stress responses, cell size, and antibiotic tolerance. Despite the widespread observation of this phenomenon in bacterial populations, not much is known about the molecular mechanisms behind phenotypic heterogeneity. Currently, our understanding is primarily limited to transcriptional profile of single cells using fluorescence reporters. Although the development of these tools has been extremely informative, it cannot fully explain the heterogeneity seen in populations. In a recent publication, Fan et al. have developed a dual-fluorescent reporter system that is capable of quantitatively measuring translational fidelity in single cells. It is shown that translational fidelity is heterogeneous and affects the growth characteristics of single cells. The development of tools for analysis of molecular heterogeneity downstream of transcription may play an important role in advancing our understanding of the physiology of bacterial populations.

Lines, loops and spirals: an intraclonal continuum of host location behaviours in walking aphids

A given animal species may employ various strategies to make searching for resources more efficient. In clonal species, in which a parent and its offspring share identical genetic information, survival of even one individual can still ensure the survival of the colony. Thus, clonal species should display a variety of resource-searching strategies rather than discrete behaviours to counter an unknown environment. However, previous studies of host location behaviours of aphids that have dropped from their host plant identified two discrete behaviours: walking in a straight line and turning frequently to search for a nearby plant. We analysed the course characteristics of individuals originating from a single genetic clone of pea aphids, Acyrthosiphon pisum, that dropped to the ground from their host plant. We found that the use of high-resolution behaviour analysis is crucial in determining whether a behavioural phenotype is continuous or discrete. In contrast to previous studies, we found a wide continuum of walking behaviours. While some aphids progressed in a straight line, moving quickly away from the dropping point, others walked in paths with increasing levels of tortuosity. Tortuous paths were characterized by a series of loops (2–18 per path), presumably to locate nearby plants. Each loop took the aphid further from its dropping location. Aphids increased the speed of their searching, so that each loop took the same time to complete. Aphids performing fewer loops increased their speed more rapidly, hinting that the number of loops an aphid performs is determined at the outset of its movement. Aphids performing more loops were more inclined to climb a new host plant. This intraclonal continuum allows dropping aphids to counter the uncertainty of a new and possibly hazardous environment and maximize the probability that at least some individuals will survive and form a new colony.

37 NORMALITY OF NEONATAL REFLEX IN CLONED DOGS

Since the birth of the world’s first cloned dog, Snuppy, somatic cell nuclear transfer (SCNT) has been a useful tool to propagate the dogs with identical genetic information. However, it is known that cloned animals sometimes exhibit phenotypic instability or abnormality. There have been few investigations about the normality of the neonatal reflex in cloned animals. Therefore, the objective of this study was to evaluate the neonatal reflex in 3 breeds of cloned dogs including shepherd, retriever, and beagle from birth to 28 days of age. Through SCNT, 8 cloned dogs were produced. After birth, 3 types of neonatal reflexes were examined and scored. For examining the flexor dominance reflex, neonatal cloned dogs were held upright and the flexor position of the limb was scored. To evaluate the withdrawal and crossed extensor reflexes, neonates were placed in lateral recumbence and their forelimbs were allowed to relax. Then, the distal forelimbs were pinched and responses were scored according to the frequency and intensity (strong = score 2, variable = score 1, and absent = score 0). The standard responses of neonates were referred from Lindsay et al. (2000 Handbook of Applied Dog Behavior and Training 1, 31–47). Descriptive analysis was used, which was based on the scores from 3 referees who evaluated the videos. The flexor dominance reflex could not be observed (score 0.0) in shepherd by Day 8, in beagle by Day 14 and in retriever by Day 16. Withdrawal reflex began to decrease on Day 22 with score 1.8 for beagle and retriever but decreased in shepherd starting on Day 24 with score 1.8. Crossed extensor reflex for shepherd started to disappear on Day 14 with score 1.5 and completely disappeared (score 0.0) on Day 22; for beagle started to disappear on Day 16 with score 1.8 and was still found until Day 28 with score 1.1; for retriever started to disappear on Day 20 and 28 with score 1.7 and 0.7, respectively. Flexor dominance reflex disappeared in cloned shepherd at a similar time to standard but beagle and retriever seem delayed 6 to 8 days compared with the reference. Withdrawal reflex in all breeds showed normal changes that should persist until adulthood. Cross extensor reflex in shepherd was close to reference but in beagle and retriever was delayed beyond Day 28; this reflex should disappear before adulthood. This study demonstrated that normal neonatal reflexes were identified in the cloned dogs, with some variations among breed. To adapt neonatal reflex as a marker to confirm phenotypic normality in cloned dogs, further investigation using various breeds of cloned dogs and greater numbers of subjects is needed. This study was supported by IPET (#316002-05-1-SB010), RDA (#PJ010928032016), Research Institute for Veterinary Science, Natural Balance Korea and the BK21 plus program.

Genetic Modification in Human Pluripotent Stem Cells by Homologous Recombination and CRISPR/Cas9 System.

Genetic modification is an indispensable tool to study gene function in normal development and disease. The recent breakthrough of creating human induced pluripotent stem cells (iPSCs) by defined factors (Takahashi et al., Cell 131:861-872, 2007) provides a renewable source of patient autologous cells that not only retain identical genetic information but also give rise to many cell types of the body including neurons and glia. Meanwhile, the rapid advancement of genome modification tools such as gene targeting by homologous recombination (Capecchi, Nat Rev Genet 6:507-512, 2005) and genome editing tools such as CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system, TALENs (Transcription activator-like effector nucleases), and ZFNs (Zinc finger nucleases) (Wang et al., Cell 153:910-918, 2013; Mali et al., Science 339:823-826, 2013; Hwang et al., Nat Biotechnol 31:227-229, 2013; Friedland et al., Nat Methods 10(8):741-743, 2013; DiCarlo et al., Nucleic Acids Res 41:4336-4343, 2013; Cong et al., Science 339:819-823, 2013) has greatly accelerated the development of human genome manipulation at the molecular level. This chapter describes the protocols for making neural lineage reporter lines using homologous recombination and the CRISPR/Cas system-mediated genome editing, including construction of targeting vectors, guide RNAs, transfection into hPSCs, and selection and verification of successfully targeted clones. This method can be applied to various needs of hPSC genetic engineering at high efficiency and high reliability.

Chromosome-specific nonrandom sister chromatid segregation during stem-cell division

Adult stem cells undergo asymmetric cell division to self-renew and give rise to differentiated cells that comprise mature tissue1. Sister chromatids may be distinguished and segregated non-randomly in asymmetrically dividing stem cells2, although the underlying mechanism and the purpose it may serve remain elusive. We developed the CO-FISH (chromosome orientation fluorescence in situ hybridization) technique3 with single-chromosome resolution and show that sister chromatids of X and Y chromosomes, but not autosomes, are segregated non-randomly during asymmetric divisions of Drosophila male germline stem cells (GSCs). This provides the first direct evidence that two sister chromatids containing identical genetic information can be distinguished and segregated non-randomly during asymmetric stem cell divisions. We further show that the centrosome, SUN-KASH nuclear envelope proteins, and Dnmt2 are required for non-random sister chromatid segregation. Our data suggest that the information on X and Y chromosomes that enables non-random segregation is primed during gametogenesis in the parents. Moreover, we show that sister chromatid segregation is randomized in GSC overproliferation and dedifferentiated GSCs. We propose that non-random sister chromatid segregation may serve to transmit distinct information carried on two sister chromatids to the daughters of asymmetrically dividing stem cells.

Emerging roles for chromatin as a signal integration and storage platform

Cells of a multicellular organism, all containing nearly identical genetic information, respond to differentiation cues in variable ways. In addition, cells are plastic, able to execute their specialized function while maintaining the ability to adapt to environmental changes. This is achieved through multiple mechanisms, including the direct regulation of chromatin-based processes in response to stimuli. How signal transduction pathways directly communicate with chromatin to change the epigenetic landscape is poorly understood. The preponderance of covalent modifications on histone tails coupled with a relatively small number of functional outputs raises the possibility that chromatin acts as a site of signal integration and storage.

Mammalian epigenetics in biology and medicine

In modern biology, Mendelian genetics provides a magnificent framework to deal with the causal relationship between genetic mutations and biological phenotypes, thus greatly promoting our understanding of developmental process of plants and animals. By analysing such mutants, as well as the etiology of human genetic diseases, we can identify the responsible genes. This type of thinking provided strong arguments for the human genome project, starting in the 1990s following several genome projects of other simpler organisms. The genome comprises all the genes in the organism and is a blueprint controlling development, growth and behaviour. That is why discovery of genomic imprinting in 1984 had such a great impact on modern biology. It is a clear exception to the simple Mendelian genetics described earlier and demonstrated that epigenetic mechanisms also play essential roles in the mammalian developmental systems. Several exceptions to Mendelian rules had already been reported in plants and insects. Genomic imprinting is an epigenetic mechanism regulating parental origin-specific gene regulation of certain subsets of genes, called imprinted genes. X chromosome inactivation is another mammalian-specific epigenetic mechanism, involving gene dosage compensation of genes on the sex chromosomes. It also plays an essential role in early mammalian development, although similar but different gene dosage mechanisms are known in other organisms. These examples clearly reveal that the mammalian genome inherits epigenetic information as ‘parental memories’ to the next generation as well as genetic information without DNA sequence alteration. These give a clear message: epigenetics is one of the fundamentals in modern biology. The birth of Dolly the sheep in 1996, the first cloned mammal from a somatic cell, is another epoch-making event in our understanding of mammalian biology, demonstrating that even terminally differentiated somatic cells can be reprogrammed in unfertilized eggs and regain totipotency of development to term. This, combined with the successful somatic cloning of several other mammalian species, provided conclusive evidence that development is operated by reversible epigenetic memories. The developmental process, in which fertilized eggs develop into multiple highly differentiated adult cells, was described by Waddington as ‘epigenetics’ to deal the phenotypic diversity of differentiated cells having identical genetic information. However, such epigenetic processes have long been considered as irreversible or one-way. Somatic cloning dramatically changed that. Epigenetics deals with heritable and reversible memories written in the genome that affect phenotypes without DNA sequence alteration. The production of induced pluripotent stem cells (iPS cells) in 2006 provided additional evidence that terminally differentiated somatic cells can be reprogrammed artificially, in this case by adding four transcription factors that play essential roles in maintaining stem cell features in embryonic stem cells (ES cells). Such transcription factors can break an epigenetic barrier formed by the action of DNA methylation, histone modification and chromatin-remodelling factors that determine each specific somatic cell type. In the famous ‘epigenetic landscape’ proposed by Waddington, it was suggested that genetic networks, as well as protein–protein interaction, underlie the formation of epigenetic landscape. DNA methylation, histone modification and chromatin remodelling factors are key players in epigenetic regulation. However, these factors may also be involved in ‘transient’ rather than ‘stable’ gene expression regulation; thus, the definition of epigenetics becomes a little bit vague and/or broader than the original one. Nevertheless, we can say that what is important for elucidating the developmental process is research on the interaction between genetic (transcription network) and epigenetic processes. Epigenetics is deeply involved in development and differentiation, and it is probable that it plays some essential roles in adaptive responses and evolutionary processes. We are now starting to understand how epigenetic state is altered in many of diseases and to recognize the slight differences that exist even between ES cells and iPS cells. That is why epigenetics is having considerable impact in the field of lifestyle-related diseases, reproductive and regenerative medicine. It is a big challenge to control cellular activities by regulating genetic and epigenetic factors and may be one of the most difficult barriers confronting present and future medicine. However, this is a necessary step towards safe and effective medicine. Several experts kindly contributed to this special issue entitled ‘mammalian epigenetics in biology and medicine’, by taking care of important topics on (i) epigenetic aspects in mammalian development [1–5], (ii) molecular mechanisms working in mammalian life cycle [6–9], and (iii) epigenetics in reprogramming technologies, human health and medicine [10–14]. We are sure that readers of this issue will gain an understanding of how important epigenetics is as one of the central issues in the biology and medicine in the twenty-first century.

Spatial epigenetics: linking nuclear structure and function in higher eukaryotes

Eukaryotic cells are defined by the genetic information that is stored in their DNA. To function, this genetic information must be decoded. In doing this, the information encoded in DNA is copied first into RNA, during RNA transcription. Primary RNA transcripts are generated within transcription factories, where they are also processed into mature mRNAs, which then pass to the cytoplasm. In the cytoplasm these mRNAs can finally be translated into protein in order to express the genetic information as a functional product. With only rare exceptions, the cells of an individual multicellular eukaryote contain identical genetic information. However, as different genes must be expressed in different cell types to define the structure and function of individual tissues, it is clear that mechanisms must have evolved to regulate gene expression. In higher eukaryotes, mechanisms that regulate the interaction of DNA with the sites where nuclear functions are performed provide one such layer of regulation. In this chapter, I evaluate how a detailed understanding of nuclear structure and chromatin dynamics are beginning to reveal how spatial mechanisms link chromatin structure and function. As these mechanisms operate to modulate the genetic information in DNA, the regulation of chromatin function by nuclear architecture defines the concept of 'spatial epigenetics'.

Epigenetics, stem cells and epithelial cell fate

Establishment and maintenance of epigenetic profiles are essential steps of development during which stem cells, despite identical genetic information, will acquire different and selective gene expression patterns, specific for their fate. This highly complex programming process involves mechanisms that are not yet completely understood although it has been established over the past few years that chromatin modifier enzymes (i.e. DNA and histone methyltransferases, histone deacetylases, histone demethylases, histone acetyltransferases) play essential roles in the establishment of transcriptional programs accompanying cell differentiation. Investigators in this field have been studying a wide variety of cell types including neural, muscular, mesenchymal and blood cells. This review will focus on epithelial cells of the digestive tract, intestinal stem cell niches being a model of choice to understand how epigenetic changes can drive nuclear programming and specific cell differentiation. Moreover, deregulation of epigenetic programming is frequently observed in human tumours and therefore, decoding these molecular mechanisms is essential to better understand both developmental and cancerous processes.

MicroRNAs and cancer

The Nobel Prize in Medicine and Physiology was awarded to the RNA interference (RNAi) field in 2006 because of the huge therapeutic potential this technique harbours. However, the RNAi technology is based on a natural mechanism that utilizes short noncoding RNA molecules (microRNAs) to regulate gene expression. This paper reviews our current knowledge about microRNAs focusing on their involvement in cancer and their potential as diagnostics and therapeutics.

Regulation of Stem Cell Differentiation by Histone Methyltransferases and Demethylases

The generation of different cell types from stem cells containing identical genetic information and their organization into tissues and organs during development is a highly complex process that requires defined transcriptional programs. Maintenance of such programs is epigenetically regulated and the factors involved in these processes are often essential for development. The activities required for cell-fate decisions are frequently deregulated in human tumors, and the elucidation of the molecular mechanisms that regulate these processes is therefore important for understanding both developmental processes and tumorigenesis.

Reprogramming of Somatic Cell Identity

All mammalian somatic cells originate from a single fertilized cell, the zygote, and share identical genetic information despite the dramatic changes in cell structure and function that accompany organismal development. The genome is subjected to a wide array of epigenetic modifications during lineage specification, a process that contributes to the implementation and maintenance of specific gene expression programs in somatic cells. Nuclear transfer and cell-fusion experiments demonstrate that the epigenetic signature directing a cell identity can be erased and modified into that of another cell type. Furthermore, in the case of cloning, differentiated cells can be reprogrammed back to pluripotency to support the reexpression of all developmental programs. Recent breakthroughs highlight the importance of transcription factors as well as epigenetic modifiers in the establishment, maintenance, and rewiring of cell identity. By focusing on reprogramming of terminally differentiated lymphocytes, we review and highlight recent insights into the molecular mechanisms and cellular events potentially underlying programming and reprogramming of somatic cell identity in mammals.