Improved vector toolkit for genome writing in mammalian cells.

Nicotinamide adenine dinucleotide (NAD+) plays a key role in cellular metabolism and signaling. In recent years, evidence has accumulated that NAD+-dependent processes are involved in the regulation of pluripotency and differentiation of mammalian embryonic stem cells. The major means to maintain NAD+ levels in mammalian cells is through its biosynthesis from various forms of vitamin B3. In this study, we examined how stimulation and inhibition of NAD+ biosynthesis affect the maintenance of the pluripotency of mouse embryonic stem cells E14 Tg2a (E14 cells). The pluripotency status of E14 cells was assessed by immunocytochemical and immunoblotting analysis using antibodies to the pluripotency factor Oct4, as well as by staining for alkaline phosphatase. Using NMR spectroscopy, we have found that the concentration of NAD+ in pluripotent E14 cells cultured in the presence of LIF is about 4 nmol/mg, and it remains unchanged after induction of differentiation with retinoic acid. We have also demonstrated that pharmacological stimulation of NAD+ biosynthesis by nicotinamide riboside increases the level of intracellular NAD+ by 20%, but it does not affect the maintenance of pluripotency in E14 cells. Moreover, under conditions of critical depletion of NAD+ pool by Nampt inhibition with FK866 E14 cells maintained pluripotency, though the expression level of Oct4 was decreased.

Stem cells have been identified in a number of mammalian tissues (e.g. bone marrow, muscle, gut, skin, and neural tissues). Until recently, it was generally believed that the differentiation potential of a mammalian somatic stem cell is restricted to one tissue only, as in the case of hematopoietic stem cells differentiating into hematopoietic cells. In this sense, somatic stem cells are limited in their differentiation potential. Several lines of evidence now challenge the idea of unilateral development. New reports show mammalian somatic stem cells can, in the course of regeneration, repopulate heterologous cell systems and therefore possess a surprisingly broad spectrum of differentiation potential. Thus, mammalian stem cells are apparently capable of fate changes between stem cell systems, although the mechanisms leading to such changes are unclear. Mechanistic models for fate changes have been proposed in Drosophila, specifically for transdetermination of imaginal discs. Imaginal discs of the larva are the primordia of the adult exoskeleton and appendages, for example, legs, and antennae. Transplantation experiments of imaginal discs have shown that discs are determined for their disc identity. Transdetermination in Drosophila refers to cases when, after regenerative cell divisions, imaginal disc cells change from one state of determination to another, initiating a pathway of differentiation leading to structures other than those corresponding to the initial state or determination; for example, an antennal imaginal disc transdetermines to a leg imaginal disc. A fate change is thus possible in both mammalian somatic stem cells and Drosophila imaginal discs following transplantation and subsequent proliferation. Here we summarize and compare observations made in such cases of stem cell and imaginal disc differentiation.

Musashi-mediated mRNA translational control has been implicated in the promotion of physiological and pathological stem cell proliferation. During self-renewal of mammalian stem cells, Musashi has been proposed to act to repress the translation of mRNAs encoding inhibitors of cell cycle progression. By contrast, in maturing Xenopus oocytes Musashi activates translation of target mRNAs that encode proteins promoting cell cycle progression. The mechanisms directing Musashi to differentially control mRNA translation in mammalian stem cells and Xenopus oocytes is unknown. In this study, we demonstrate that the mechanisms defining Musashi function lie within the cellular context. Specifically, we show that murine Musashi acts as an activator of translation in maturing Xenopus oocytes while Xenopus Musashi functions as a repressor of target mRNA translation in mammalian cells. We further demonstrate that within the context of a primary mammalian neural stem/progenitor cell, Musashi can be converted from a repressor of mRNA translation to an activator of translation in response to extracellular stimuli. We present current models of Musashi-mediated mRNA translational control and discuss possible mechanisms for regulating Musashi function. An understanding of these mechanisms presents exciting possibilities for development of therapeutic targets to control physiological and pathological stem cell proliferation.

Radiation therapy (RT) often damages healthy tissues, limiting the dosage level and tumor damage potential due to single-strand and double-strand breaks in the DNA, leading to apoptosis. Therefore, this study aims to investigate the transcriptomic differences between planarian Neoblasts (NBs) and mammalian bone marrow mesenchymal stem cells (bmMSCs) to identify key genes in the ionizing radiation (IR) response pathway. NBs are extracted from Schmidtea mediterranea and bmMSCs from C57BL/6 mice and human donors. RNA sequencing (RNA-seq) is performed on the cell post-IR to identify differentially expressed genes. Techniques such as BLAST, DESeq2, and OrthoFinder identify homologs and unique genes. Gene ontology (GO) analysis, RNA interference (RNAi), and Clustered Regularly Interspaced Short Palindromic Repeats-Cas9 (CRISPR-Cas9) study the impact of manipulating these genes on IR tolerance by indirectly validating the function of the candidate genes. This study expects to be able to isolate cell populations and identify differentially expressed genes (DEGs) related to IR tolerance across the three models. Meanwhile, phylogenetic analyses model the evolutionary relationships between conserved and unique genes, providing insight into fundamental cellular processes and alternative pathways for therapeutic intervention. Comparative genomic techniques facilitated the identification and functional validation of homologs and unique genes. However, the holistic identification of candidate genes is limited by the inability to uncover detailed signaling pathways and mode limitations.

Keywords: : mesenchymal stem cellspluripotency transcription factorOct4NanogDnmt1self-renewalproliferationspontaneous differentiation

Manipulating piggyBac Transposon Chromosomal Integration Site Selection in Human Cells

An Asymmetrically Localized Staufen2-Dependent RNA Complex Regulates Maintenance of Mammalian Neural Stem Cells

Although CpG dinucleotides remain the primary site for DNA methylation in mammals, there is emerging evidence that DNA methylation at non-CpG sites (CpA, CpT and CpC) is not only present in mammalian cells, but may play a unique role in the regulation of gene expression. For some time it has been known that non-CpG methylation is abundant in plants and present in mammalian embryonic stem cells, but non-CpG methylation was thought to be lost upon cell differentiation. However, recent publications have described a role for non-CpG methylation in adult mammalian somatic cells including the adult mammalian brain, skeletal muscle, and hematopoietic cells and new interest in this field has been stimulated by the availability of high throughput sequencing techniques that can accurately measure this epigenetic modification. Genome wide assays indicate that non-CpG methylation is negligible in human fetal brain, but abundant in human adult brain tissue. Genome wide measurement of non-CpG methylation coupled with RNA-Sequencing indicates that in the human adult brain non-CpG methylation levels are inversely proportional to the abundance of mRNA transcript at the associated gene. Additionally specific examples where alterations in non-CpG methylation lead to changes in gene expression have been described; in PGC1α in human skeletal muscle, IFN-γ in human T-cells and SYT11 in human brain, all of which contribute to the development of human disease.

In the preimplantation mammalian embryo, cells of the inner cell mass can differentiate into any cell type present in the more mature embryo. As of 1981, in mice and 1998 in humans, it has been recognized that embryonic stem cells (ESCs) with a prolonged proliferative capacity can be derived from the inner cell mass in vitro (Evans and Kaufman 1981; Thomson, Itskovitz-Eldor et al. 1998). ESCs are pluripotent cells that can contribute to all tissues in vivo and to the three primary germ layers as well as extraembryonic tissues in vitro. Because pluripotency is maintained in these cells even after prolonged periods of culture, human ESCs have great therapeutic potential for tissue regeneration. Indeed, embryonic and adult stem cells (SCs) hold great promise for regenerative medicine, tissue repair, and gene therapy. Careful molecular characterization of embryonic pluripotency should help to optimize and scale up the in vitro production of ESCs for clinical applications. The mechanisms regulating self-renewal and cell fate decisions in mammalian stem cells are poorly understood. As compared with differentiated cell types, stem cells express a significantly higher number of genes (represented by expressed sequence tags) of unknown function. The properties that distinguish stem cells from other cells are largely unknown, and the identification of signals that regulate stem cell differentiation remains fundamental to our understanding of cellular diversity. Embryonic and adult stem cells have many similarities at the transcriptional level. The overlapping set of expressed gene products represents a molecular signature of stem cells (Bhattacharya, Miura et al. 2004; Assou, Le Carrour et al. 2007). A list of human and mouse genes involved in stemness has been generated (Assou, Le Carrour et al. 2007) and includes 92 stemness genes known to be expressed in mouse or human ESCs, e.g., OCT3/4, NANOG, Cripto/TDGFI, Cx43 and Galanin (Richards, Tan et al. 2004). Work in the field of embryogenesis has also contributed to our understanding of the function of these pluripotency-associated genes. The four most significantly overexpressed genes in undifferentiated embryonic tissues are Galanin, POU5FI, NANOG and DPPA4 (Zeng, Miura et al. 2004). In most studies, galanin has been highlighted as the most abundant transcript in ES culture as well as human and rodent embryonic tissues (Anisimov, Tarasov et al. 2002; Zeng, Miura et al. 2004). Both galanin and galanin receptors are expressed in ES cells, indicating a potential functional role for this protein (Tarasov, Tarasova et al. 2002). This chapter will be devoted to a description of the galanin expression profiles in embryonic tissues and stem cells as well as its possible functional role.

Profoundly different patterns of potency and division are exhibited by mammalian embryonic and adult stem cells. Additional confusion surrounds stem-cell surrogates, cache and reserve cells having some characteristics of stem cells and not others. Mystification may have been introduced historically with the concepts of determinate and regulative development, but, hopefully, the muddle can be resolved by tracing the evolution of stem cells in Metazoa. Blastomeres in marine sponges, cnidarians, lophotrochozoans, small ecdysozoans (e.g., Caenorhabditis elegans), and some deuterostomes (e.g., echinoderms and ascidians) exhibit determinative development. Their larval and adult cells have narrow potencies, sometimes coupled to virtually unlimited proliferation, and function in the growth, maintenance and regulation of body size. The embryos of larger arthropods and deuterostomes with well-provisioned eggs or viviparity, on the other hand, exhibit regulative development, while their larval "set-aside" or adult stem cells function in the growth, maintenance, and regulation of organ size coupled to constrained proliferation and cell turnover. Mammalian embryonic stem cells would seem adapted to rapid proliferation, functioning in part to enclose yolk or to acquire access to maternal resources. The cellular products of embryonic stem cells routinely come under global influences and give rise to the cells of germ layers and organ rudiments. Mammalian adult stem cells resemble the blastomeres of planktonic and benthic organisms with small eggs and may have evolved in mature organisms as an adaptation to the growth and maintenance of tissues via proliferation and the regulation of organ size via cell loss (e.g., terminal differentiation). Cancer stem cells, instrumental in metastasis, would seem to ignore mechanisms normally functioning in the removal of excess cells. Strategies for regenerative therapies in adult mammals, therefore, might be based on stimulating growth of adult stem cells or their surrogates in specific tissues rather than on introducing embryonic stem cells into adults. Likewise, strategies for the containment of cancer might be based on promoting normal pathways of cell loss, the basal mode for handling excess cells.

Monoallelic gene expression occurs in various mammalian cells and can be regulated genetically, epigenetically and/or stochastically. We identified 145 monoallelically expressed genes (MoEGs), including seven known imprinted genes, in mouse embryonic stem cells (ESCs) derived from reciprocal F1 hybrid blastocysts and cultured in 2i/LIF. As all MoEGs except for the imprinted genes were expressed in a genetic-origin-dependent manner, we focused on this class of MoEGs for mechanistic studies. We showed that a majority of the genetic-origin-dependent MoEGs identified in 2i/LIF ESCs remain monoallelically expressed in serum/LIF ESCs, but become more relaxed or even biallelically expressed upon differentiation. These MoEGs and their regulatory regions were highly enriched for single nucleotide polymorphisms. In addition, some MoEGs were associated with retrotransposon insertions/deletions, consistent with the fact that certain retrotransposons act as regulatory elements in pluripotent stem cells. Interestingly, most MoEGs showed allelic differences in enrichment of histone H3K27me and H3K4me marks, linking allelic epigenetic differences and monoallelic expression. In contrast, there was little or no allelic difference in CpG methylation or H3K9me. Taken together, our study highlights the impact of genetic variation including single nucleotide polymorphisms and retrotransposon insertions/deletions on monoallelic epigenetic marks and expression in ESCs.

Biallelic targeting of expressed genes in mouse embryonic stem cells using the Cas9 system

Wnts comprise a family of 20 lipid-modified glycoproteins in mammals and play critical roles during embryological development and organogenesis of several organ systems, including the heart. They are required for mesoderm formation and have been implicated in promoting cardiomyogenic differentiation of mammalian embryonic stem cells, but the underlying mechanisms regulating Wnt signaling during cardiomyogenesis remain poorly understood. In this report, we show that in a pluripotent mouse embryonal carcinoma stem cell line, SFRP2 inhibits cardiomyogenic differentiation by regulating Wnt3a transcription. SFRP2 inhibited early stages of cardiomyogenesis, preventing mesoderm specification and maintaining the cells in the undifferentiated state. Using a gain- and loss-of-function approach, we demonstrate that although addition of recombinant SFRP2 decreased Wnt3a transcription and cardiomyogenic differentiation, silencing of Sfrp2 led to enhanced Wnt3a transcription, mesoderm formation, and increased cardiomyogenesis. We show that the inhibitory effects of SFRP2 on Wnt transcription are secondary to interruption of a positive feedback effect of Wnt3a on its own transcription. Wnt3a increased its own transcription via the canonical pathway and TCF4 family of transcription factors, and the inhibitory effects of SFRP2 on Wnt3a transcription were associated with disruption of downstream canonical Wnt signaling. The inhibitory effects of Sfrp2 on Wnt3a expression identify Sfrp2 as a "checkpoint gene," which exerts its control on cardiomyogenesis through regulation of Wnt3a transcription.

The auxin-inducible degron (AID) system is a promising tool for dynamic protein degradation. In mammalian cells, this approach has become indispensable to study fundamental molecular functions, such as replication, chromatin dynamics, or transcription, which are otherwise difficult to dissect. We present evaluation of the two prominent AID systems based on OsTIR1 and AtAFB2 auxin receptor F-box proteins (AFBs). We analyzed degradation dynamics of cohesin/condensin complex subunits in mouse embryonic stem cells (Rad21, Smc2, Ncaph, and Ncaph2) and human haploid HAP1 line (RAD21, SMC2). Double antibiotic selection helped achieve high homozygous AID tagging of an endogenous gene for all genes using CRISPR/Cas9. We found that the main challenge for successful protein degradation is obtaining cell clones with high and stable AFB expression levels due to the mosaic expression of AFBs. AFB expression from a transgene tends to decline with passages in the absence of constant antibiotic selection, preventing epigenetic silencing of a transgene, even at the AAVS1 safe-harbor locus. Comparing two AFBs, we found that the OsTIR1 system showed weak dynamics of protein degradation. At the same time, the AtAFB2 approach was very efficient even in random integration of AFB-expressed transgenes. Other factors such as degradation dynamics and low basal depletion were also in favor of the AtAFB2 system.

Chromosome rearrangements, such as large deletions, inversions, or translocations, mediate migration of large DNA segments within or between chromosomes, which can have major effects on cellular genetic control. A method for chromosome manipulation would be very useful for studying the consequences of large-scale DNA rearrangements in mammalian cells or animals. With the use of the Cre-loxP recombination system of bacteriophage P1, we induced a site-specific translocation between the Dek gene on chromosome 13 and the Can gene on chromosome 2 in mouse embryonic stem cells. The estimated frequency of Cre-mediated translocation between the nonhomologous mouse chromosomes is approximately 1 in 1200-2400 embryonic stem cells expressing Cre recombinase. These results demonstrate the feasibility of site-specific recombination systems for chromosome manipulation in mammalian cells in vivo, breaking ground for chromosome engineering.