Use of UTF1 genetic control elements as iPSC reporter

Complex haploinsufficiency in pluripotent cells yields somatic cells with DNA methylation abnormalities and pluripotency induction defects

A complete knockout of a single key pluripotency gene may drastically affect embryonic stem cell function and epigenetic reprogramming. In contrast, elimination of only one allele of a single pluripotency gene is mostly considered harmless to the cell. To understand whether complex haploinsufficiency exists in pluripotent cells, we simultaneously eliminated a single allele in different combinations of two pluripotency genes (i.e., Nanog+/-;Sall4+/-, Nanog+/-;Utf1+/-, Nanog+/-;Esrrb+/- and Sox2+/-;Sall4+/-). Although these double heterozygous mutant lines similarly contribute to chimeras, fibroblasts derived from these systems show a significant decrease in their ability to induce pluripotency. Tracing the stochastic expression of Sall4 and Nanog at early phases of reprogramming could not explain the seen delay or blockage. Further exploration identifies abnormal methylation around pluripotent and developmental genes in the double heterozygous mutant fibroblasts, which could be rescued by hypomethylating agent or high OSKM levels. This study emphasizes the importance of maintaining two intact alleles for pluripotency induction.

An Insight into the Role of UTF1 in Development, Stem Cells, and Cancer

The curiosity to understand the mechanisms regulating transcription in pluripotent cells resulted in identifying a unique transcription factor named Undifferentiated embryonic cell transcription factor 1 (UTF1). This proline-rich, nuclear protein is highly conserved among placental mammals with prominent expression observed in pluripotent, germ, and cancer cells. In pluripotent and germ cells, its role has been implicated primarily in proper cell differentiation, whereas in cancer, it shows tissue-specific function, either as an oncogene or a tumor suppressor gene. Furthermore, UTF1 is crucial for germ cell development, spermatogenesis, and maintaining male fertility in mice. In addition, recent studies have demonstrated the importance of UTF1 in the generation of high quality induced Pluripotent Stem Cells (iPSCs) and as an excellent biomarker to identify bona fide iPSCs. Functionally, UTF1 aids in establishing a favorable chromatin state in embryonic stem cells, reducing "transcriptional noise" and possibly functions similarly in re-establishing this state in differentiated cells upon their reprogramming to generate mature iPSCs. This review highlights the multifaceted roles of UTF1 and its implication in development, spermatogenesis, stem, and cancer cells.

Utf1 contributes to intergenerational epigenetic inheritance of pluripotency

Undifferentiated embryonic cell transcription factor 1 (Utf1) is expressed in pluripotent embryonic stem cells (ESCs) and primordial germ cells (PGCs). Utf1 expression is directly controlled by pluripotency factors Oct4 and Sox2, which form a ternary complex with the Utf1 enhancer. The Utf1 protein plays a role in chromatin organization and epigenetic control of bivalent gene expression in ESCs in vitro, where it promotes effective cell differentiation during exit from pluripotency. The function of Utf1 in PGCs in vivo, however, is not known. Here, we report that proper development of Utf1 null embryos almost entirely depends on the presence of functional Utf1 alleles in the parental germline. This indicates that Utf1’s proposed epigenetic role in ESC pluripotency in vitro may be linked to intergenerational epigenetic inheritance in vivo. One component - or at least facilitator - of the relevant epigenetic mark appears to be Utf1 itself, since Utf1-driven tomato reporter and Utf1 are detected in mature germ cells. We also provide initial evidence for a reduced adult testis size in Utf1 null mice. Our findings thus point at unexpected functional links between the core ESC pluripotency factor network and epigenetic inheritance of pluripotency.

Conservative site-specific and single-copy transgenesis in human LINE-1 elements

Genome engineering of human cells plays an important role in biotechnology and molecular medicine. In particular, insertions of functional multi-transgene cassettes into suitable endogenous sequences will lead to novel applications. Although several tools have been exploited in this context, safety issues such as cytotoxicity, insertional mutagenesis and off-target cleavage together with limitations in cargo size/expression often compromise utility. Phage λ integrase (Int) is a transgenesis tool that mediates conservative site-specific integration of 48 kb DNA into a safe harbor site of the bacterial genome. Here, we show that an Int variant precisely recombines large episomes into a sequence, term edattH4X, found in 1000 human Long INterspersed Elements-1 (LINE-1). We demonstrate single-copy transgenesis through attH4X-targeting in various cell lines including hESCs, with the flexibility of selecting clones according to transgene performance and downstream applications. This is exemplified with pluripotency reporter cassettes and constitutively expressed payloads that remain functional in LINE1-targeted hESCs and differentiated progenies. Furthermore, LINE-1 targeting does not induce DNA damage-response or chromosomal aberrations, and neither global nor localized endogenous gene expression is substantially affected. Hence, this simple transgene addition tool should become particularly useful for applications that require engineering of the human genome with multi-transgenes.

Probing into the biological processes influenced by ESC factor and oncoprotein HMGA2 using iPSCs

Induced pluripotent stem cells (iPSCs) are rapidly evolving into an important research tool due to their close resemblance with pluripotent embryonic stem cells (ESCs). Of particular interest at this point are iPSC applications in disease modeling and drug discovery/testing. The high mobility group AT-hook 2 (HMGA2) protein is a nonhistone chromatin factor normally expressed in ESCs and during early developmental stages. Aberrant HMGA2 expression is associated, for example, with abnormal body stature, diabetes mellitus, heart development and uterine leiomyomas. Furthermore, the protein is re-expressed in many primary tumor cells and plays an important role in metastasis. Here we used iPSC formation in conjunction with exogenous human HMGA2 expression to gain insight into biological functions of HMGA2. Gene expression profiling and gene ontology analyses showed that anatomical development and cell adhesion/differentiation processes are strongly affected by HMGA2. This could help to uncover, at the molecular level, some of the known phenotypic consequences of aberrant HMGA2 expression. Furthermore, our data showed that expression of key diabetes susceptibility genes is influenced by HMGA2, which revealed an interesting link to the recently indentified Lin28/let-7 pathway regulating mammalian glucose metabolism. Contrary to a previous report, our results indicate that HMGA2 is not involved in the regulation of telomerase gene expression. Finally, our data support a model in which tight regulation of intracellular HMGA2 levels is important both to maintain a pluripotent ESC state and to induce differentiation into certain cell lineages during later developmental stages.