DNA-induced spatial entrapment of general transcription machinery can stabilize gene expression in a nondividing cell.

An important characteristic of cell differentiation is its stability. Only rarely do cells or their stem cell progenitors change their differentiation pathway. If they do, it is often accompanied by a malfunction such as cancer. A mechanistic understanding of the stability of differentiated states would allow better prospects of alleviating the malfunctioning. However, such complete information is yet elusive. Earlier experiments performed in Xenopus oocytes to address this question suggest that a cell may maintain its gene expression by prolonged binding of cell type-specific transcription factors. Here, using DNA competition experiments, we show that the stability of gene expression in a nondividing cell could be caused by the local entrapment of part of the general transcription machinery in transcriptionally active regions. Strikingly, we found that transcriptionally active and silent forms of the same DNA template can stably coexist within the same nucleus. Both DNA templates are associated with the gene-specific transcription factor Ascl1, the core factor TBP2, and the polymerase II (Pol-II) ser5 C-terminal domain (CTD) phosphorylated form, while Pol-II ser2 CTD phosphorylation is restricted to the transcriptionally dominant template. We discover that the active and silent DNA forms are physically separated in the oocyte nucleus through partition into liquid-liquid phase-separated condensates. Altogether, our study proposes a mechanism of transcriptional regulation involving a spatial entrapment of general transcription machinery components to stabilize the active form of a gene in a nondividing cell.

The initiation and maintenance of a differentiated state in development.

Proper function of the body is maintained by an intricate interaction and communication among cells. during the animal development how these cells are formed and maintained is an important yet elusive. Understanding of how cells such as muscle and nerve cells maintain their identities would enable us to control the diseases which include malfunctioning in cellular identities such as cancer. In this article, we describe how the concept of formation and maintenance of cell identities has changed over the last 100 years. We will also briefly describe our current experimental work which includes transcriptional dynamics, and protein-protein interaction and how they are bringing new molecular insights. We also describe liquid-liquid phase separation as a potential new mechanism for the stability of gene expression in the non dvididng specialised cells of Xenopus oocytes.

Mechanisms of nuclear reprogramming by eggs and oocytes: a deterministic process?

Differentiated cells can be experimentally reprogrammed back to pluripotency by nuclear transfer, cell fusion or induced pluripotent stem cell technology. Nuclear transfer and cell fusion can lead to efficient reprogramming of gene expression. The egg and oocyte reprogramming process includes the exchange of somatic proteins for oocyte proteins, the post-translational modification of histones and the demethylation of DNA. These events occur in an ordered manner and on a defined timescale, indicating that reprogramming by nuclear transfer and by cell fusion rely on deterministic processes.

Long-term association of a transcription factor with its chromatin binding site can stabilize gene expression and cell fate commitment.

Some lineage-determining transcription factors are overwhelmingly important in directing embryonic cells to a particular differentiation pathway, such as Ascl1 for nerve. They also have an exceptionally strong ability to force cells to change from an unrelated pathway to one preferred by their action. Transcription factors are believed to have a very short residence time of only a few seconds on their specific DNA or chromatin-binding sites. We have developed a procedure in which DNA containing one copy of the binding site for the neural-inducing factor Ascl1 is injected directly into a Xenopus oocyte nucleus which has been preloaded with a limiting amount of the Ascl1 transcription factor protein. This is followed by a further injection of DNA as a competitor, either in a plasmid or in chromosomal DNA, containing the same binding site but with a different reporter. Importantly, expression of the reporter provides a measure of the function of the transcription factor in addition to its residence time. The same long residence time and resistance to competition are seen with the estrogen receptor and its DNA response elements. We find that in this nondividing oocyte, the nerve-inducing factor Ascl1 can remain bound to a specific chromatin site for hours or days and thereby help to stabilize gene expression. This stability of transcription factor binding to chromatin is a necessary part of its action because removal of this factor causes discontinuation of its effect on gene expression. Stable transcription factor binding may be a characteristic of nondividing cells.

Injected cells provide a valuable complement to cell-free systems for analysis of gene expression.

The aim of this short review is to comment on the advantages of injecting purified molecules into a normal living cell as a complement to the constitution of a cell-free system for analyzing the function of cell components. We emphasize here that the major difference is that, by injection, most components of a cell are maintained at their normal concentration, which is difficult, even if at all possible, to achieve in a cell-free system. We exemplify the benefits of a cell injection system by the efficiency and long duration of DNA transcription by RNA polymerase II, as used by most genes, and by the widespread success of injecting purified messenger RNA for protein synthesis. The most recent work using cell injection also gives a new understanding of a long lasting transcription factor residence on its DNA or chromatin not shown by other procedures. Lastly, we re-visit an old idea that transcription factors that guide cell fate may be stably bound to DNA or chromatin, except at S-phase or mitosis in the cell cycle, when they can undergo exchange with equivalent molecules in the cell.

The cloning of a frog.

It is relatively unusual for the Nobel Prize in Physiology or Medicine to be made, to a large extent, on the basis of a single author paper, published over 50 years ago, for work carried out by a graduate student. This was largely true of a paper published in 1962 in the journal Development (called at that time the Journal of Embryology and Experimental Morphology). The main subject of that paper was the production of normal tadpoles from the nuclei of intestinal epithelium cells of Xenopus laevis. In view of this unusual situation, I have been invited to comment on the 1962 paper.

The egg and the nucleus: a battle for supremacy.

Sir John Gurdon and Professor Shinya Yamanaka were the recipients of the 2012 Nobel Prize for Physiology or Medicine. This Spotlight article is a commentary on the early nuclear transplant work in Xenopus, which was very important for the Nobel award in 2012, and the influence of this work on the reprogramming field.

Nuclear reprogramming.

There is currently particular interest in the field of nuclear reprogramming, a process by which the identity of specialised cells may be changed, typically to an embryonic-like state. Reprogramming procedures provide insight into many mechanisms of fundamental cell biology and have several promising applications, most notably in healthcare through the development of human disease models and patient-specific tissue-replacement therapies. Here, we introduce the field of nuclear reprogramming and briefly discuss six of the procedures by which reprogramming may be experimentally performed: nuclear transfer to eggs or oocytes, cell fusion, extract treatment, direct reprogramming to pluripotency and transdifferentiation.

Epigenetic factors influencing resistance to nuclear reprogramming.

Patient-specific somatic cell reprogramming is likely to have a large impact on medicine by providing a source of cells for disease modelling and regenerative medicine. Several strategies can be used to reprogram cells, yet they are generally characterised by a low reprogramming efficiency, reflecting the remarkable stability of the differentiated state. Transcription factors, chromatin modifications, and noncoding RNAs can increase the efficiency of reprogramming. However, the success of nuclear reprogramming is limited by epigenetic mechanisms that stabilise the state of gene expression in somatic cells and thereby resist efficient reprogramming. We review here the factors that influence reprogramming efficiency, especially those that restrict the natural reprogramming mechanisms of eggs and oocytes. We see this as a step towards understanding the mechanisms by which nuclear reprogramming takes place.

Transcriptional regulation and nuclear reprogramming: roles of nuclear actin and actin-binding proteins.

Proper regulation of transcription is essential for cells to acquire and maintain cell identity. Transcriptional activation plays a central role in gene regulation and can be modulated by introducing transcriptional activators such as transcription factors. Activators act on their specific target genes to induce transcription. Reprogramming experiments have revealed that as cells become differentiated, some genes are highly silenced and even introduction of activators that target these silenced genes does not induce transcription. This can be explained by chromatin-based repression that restricts access of transcriptional activators to silenced genes. Transcriptional activation from these genes can be accomplished by opening chromatin, in addition to providing activators. Once a de novo transcription network is established, cells are differentiated or reprogrammed to a new cell type. Emerging evidence suggests that actin in the nucleus (nuclear actin) and nuclear actin-binding proteins are implicated in these transcriptional regulatory processes. This review summarizes roles of nuclear actin and actin-binding proteins in transcriptional regulation. We also discuss possible functions of nuclear actin during reprogramming in the context of transcription and chromatin remodeling.

Deterministic nuclear reprogramming of mammalian nuclei to a totipotency-like state by Amphibian meiotic oocytes for stem cell therapy in humans.

The ultimate aim of nuclear reprogramming is to provide stem cells or differentiated cells from unrelated cell types as a cell source for regenerative medicine. A popular route towards this is transcription factor induction, and an alternative way is an original procedure of transplanting a single somatic cell nucleus to an unfertilized egg. A third route is to transplant hundreds of cell nuclei into the germinal vesicle (GV) of a non-dividing Amphibian meiotic oocyte, which leads to the activation of silent genes in 24 h and robustly induces a totipotency-like state in almost all transplanted cells. We apply this third route for potential therapeutic use and describe a procedure by which the differentiated states of cells can be reversed so that totipotency and pluripotency gene expression are regained. Differentiated cells are exposed to GV extracts and are reprogrammed to form embryoid bodies, which shows the maintenance of stemness and could be induced to follow new directions of differentiation. We conclude that much of the reprogramming effect of eggs is already present in meiotic oocytes and does not require cell division or selection of dividing cells. Reprogrammed cells by oocytes could serve as replacements for defective adult cells in humans.

Xenopus oocytes reactivate muscle gene transcription in transplanted somatic nuclei independently of myogenic factors.

Transplantation into eggs or oocytes is an effective means of achieving the reprogramming of somatic cell nuclei. We ask here whether the provision of gene-specific transcription factors forms part of the mechanism by which a gene that is repressed in somatic cells is transcribed in oocytes. We find that M1 oocytes have an extremely strong transcription-inducing activity. They cause muscle genes of nuclei from non-muscle somatic cells, after injection into oocytes, to be transcribed to nearly the same extent as muscle genes in muscle cells. We show, surprisingly, that the myogenic factor MyoD and other known myogenic factors are not required to induce the transcription of muscle genes in a range of non-muscle somatic cell nuclei after transplantation to Xenopus oocytes. The overexpression of Id, a dominant-negative repressor of MyoD, prevents maternal MyoD from binding to its consensus sequences; nevertheless, muscle genes are activated in somatic nuclei to the same extent as without Id. We conclude that M1 oocytes can reprogram somatic nuclei in a different way to other experimental procedures: oocytes do not suppress the transcription of inappropriate genes and they activate a gene without the help of its known transcription factors. We suggest that these characteristics might be a special property of amphibian oocytes, and possibly of oocytes in general.

Nuclear exclusion of Smad2 is a mechanism leading to loss of competence.

Controlling the duration of a signalling process in development by loss of competence is important because too strong an induction can change cell fate. To understand some of the mechanisms that underlie loss of competence, we have analysed the transduction of transforming growth factor-beta (TGF-beta) signalling during mesoderm formation, which is thought to be induced by TGF-beta-like signalling, in embryos of the frog Xenopus laevis. Here we show that gastrula ectoderm has the ability to express mesodermal marker genes in response to the TGF-beta signalling molecule activin for many hours, but then loses this ability within 1 h for all mesodermal genes tested. This loss of mesodermal competence correlates with the inability of Smad2, the principal intracellular signal transducer of activin, to accumulate in the nucleus. Mutating three phosphorylation sites within Smad2 abrogates the temporal restriction of Smad2 to accumulate in the nucleus. Overexpression of this mutant form of Smad2 can prolong the competence of endogenous mesodermal genes to respond to activin signalling. Thus, restricting the subcellular localization of an intracellular signal transducer constitutes a mechanism that leads to loss of mesodermal competence. This mechanism operates within less than an hour, and is therefore well suited to control an orderly sequence of inductions.

Mammalian nuclear transplantation to Germinal Vesicle stage Xenopus oocytes - a method for quantitative transcriptional reprogramming.

Full-grown Xenopus oocytes in first meiotic prophase contain an immensely enlarged nucleus, the Germinal Vesicle (GV), that can be injected with several hundred somatic cell nuclei. When the nuclei of mammalian somatic cells or cultured cell lines are injected into a GV, a wide range of genes that are not transcribed in the donor cells, including pluripotency genes, start to be transcriptionally activated, and synthesize primary transcripts continuously for several days. Because of the large size and abundance of Xenopus laevis oocytes, this experimental system offers an opportunity to understand the mechanisms by which somatic cell nuclei can be reprogrammed to transcribe genes characteristic of oocytes and early embryos. The use of mammalian nuclei ensures that there is no background of endogenous maternal transcripts of the kind that are induced. The induced gene transcription takes place in the absence of cell division or DNA synthesis and does not require protein synthesis. Here we summarize new as well as established results that characterize this experimental system. In particular, we describe optimal conditions for transplanting somatic nuclei to oocytes and for the efficient activation of transcription by transplanted nuclei. We make a quantitative determination of transcript numbers for pluripotency and housekeeping genes, comparing cultured somatic cell nuclei with those of embryonic stem cells. Surprisingly we find that the transcriptional activation of somatic nuclei differs substantially from one donor cell-type to another and in respect of different pluripotency genes. We also determine the efficiency of an injected mRNA translation into protein.

Tpt1 activates transcription of oct4 and nanog in transplanted somatic nuclei.

Nuclear transfer to eggs or oocytes provides a potential route for cell-replacement therapies because oocytes directly reprogram transplanted mammalian somatic-cell nuclei such that they have an embryo-like pattern of gene expression. This includes a large increase in the mRNA level of the stem-cell marker gene oct4. We have developed a novel procedure to identify new proteins that greatly increase the level of oct4 mRNA upon nuclear transfer. We have isolated Xenopus oocyte proteins that bind to the regulatory region of the mouse oct4 gene and identified these by mass spectrometry. The proteins include the retinoic-acid-receptor gamma, a known repressor of oct4 transcription, and Tpt1, a cancer-associated factor. The depletion of transcripts of retinoic-acid receptor gamma from oocytes increases oct4 and nanog transcription as expected, and depletion of tpt1 transcripts in oocytes reduces oct4 and nanog transcription in injected HeLa nuclei. An elevation of tpt1 transcripts in oocytes results in an earlier activation of oct4 transcription. Therefore, we identify a novel role for tpt1 in activating pluripotency genes upon nuclear transfer. Our results help to elucidate the mechanism by which somatic-cell nuclei are reprogrammed to have an embryo-like pattern of gene expression.

Functional gap junctions are not required for muscle gene activation by induction in Xenopus embryos.

Muscle gene expression is known to be induced in animal pole cells of a Xenopus blastula after 2-3 h of close contact with vegetal pole cells. We tested whether this induction requires functional gap junctions between vegetal and animal portions of an animal-vegetal conjugate. Muscle gene transcription was assayed with a muscle-specific actin gene probe and the presence or absence of communication through gap junctions was determined electrophysiologically. Antibodies to gap junction protein were shown to block gap junction communication for the whole of the induction time, but did not prevent successful induction of muscle gene activation. The outcome was the same whether communication between inducing vegetal cells and responding animal cells was blocked by introducing antibodies into vegetal cells alone or into animal cells alone. We conclude that gap junctions are not required for this example of embryonic induction.

Identification of a regeneration-organizing cell in the Xenopus tail.

Unlike mammals, Xenopus laevis tadpoles have a high regenerative potential. To characterize this regenerative response, we performed single-cell RNA sequencing after tail amputation. By comparing naturally occurring regeneration-competent and -incompetent tadpoles, we identified a previously unrecognized cell type, which we term the regeneration-organizing cell (ROC). ROCs are present in the epidermis during normal tail development and specifically relocalize to the amputation plane of regeneration-competent tadpoles, forming the wound epidermis. Genetic ablation or manual removal of ROCs blocks regeneration, whereas transplantation of ROC-containing grafts induces ectopic outgrowths in early embryos. Transcriptional profiling revealed that ROCs secrete ligands associated with key regenerative pathways, signaling to progenitors to reconstitute lost tissue. These findings reveal the cellular mechanism through which ROCs form the wound epidermis and ensure successful regeneration.

The community effect, dorsalization and mesoderm induction.

The community effect is an interaction among muscle progenitor cells of amphibian gastrula, and is necessary for the initiation of muscle-specific gene expression. Dorsalization provides a signal that can convert ventral mesoderm cells to a muscle fate. Neither process involves mesoderm-inducing molecules. We suggest that the developmental significance of the community effect is to generate homogeneous but clearly demarcated groups of cells from progenitor cells arranged in a continuous gradient of developmental potential.

Markers of vertebrate mesoderm induction.

Mesoderm formation is the first major differentiative event in vertebrate development. Many new mesoderm-specific genes have recently been described in the mouse, chick, frog and fish and belong to classes comprising T-domain genes, homeobox genes and those encoding secreted proteins. The T-domain genes have different but overlapping expression patterns and, in Xenopus, can ectopically activate nearly all other mesodermal genes. Several new homebox genes seem to mediate the ventralising activity of bone morphogenetic protein. New genes encoding secreted proteins induce dorsal mesoderm, in some cases by antagonizing ventralising factors.